[Federal Register Volume 59, Number 4 (Thursday, January 6, 1994)]
[Proposed Rules]
[Pages 810-871]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 94-120]


[[Page Unknown]]

[Federal Register: January 6, 1994]


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Part II

Environmental Protection Agency
_______________________________________________________________________



40 CFR Part 131



Sacramento River, San Joaquin River, and San Francisco Bay and Delta, 
CA; Water Quality Standards for Surface Water; Proposed Rule



_______________________________________________________________________
Department of the Interior



Fish and Wildlife Service



_______________________________________________________________________



50 CFR Part 17



Endangered and Threatened Wildlife and Plants: Delta Smelt, Sacramento 
Splittail, and Longfin Smelt; Proposed Rules
ENVIRONMENTAL PROTECTION AGENCY

40 CFR Part 131

[OW-FRL-4783-6]

 

Water Quality Standards for Surface Waters of the Sacramento 
River, San Joaquin River, and San Francisco Bay and Delta of the State 
of California

AGENCY: Environmental Protection Agency.

ACTION: Proposed rule.

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SUMMARY: On September 3, 1991, the Regional Administrator for Region IX 
of the U.S. Environmental Protection Agency disapproved certain water 
quality criteria contained in the Water Quality Control Plan for 
Salinity for the San Francisco Bay/Sacramento-San Joaquin Delta 
Estuary, that was adopted by the California State Water Resources 
Control Board on May 1, 1991. These criteria were disapproved because 
they failed to protect the Estuarine Habitat and other designated fish 
and wildlife uses of the estuary. Under the authority of section 303 of 
the Clean Water Act, this document proposes a rule establishing three 
sets of federal criteria to protect the designated uses of the estuary: 
salinity criteria protecting the Estuarine Habitat and other designated 
fish and wildlife uses, a second set of salinity criteria (measured in 
electrical conductivity) to protect the Fish Spawning (Striped Bass) 
designated use in the lower San Joaquin River, and a set of salmon 
smolt survival index criteria to protect the Fish Migration and Cold 
Fresh-Water Habitat designated uses in the estuary.

DATES: All written comments received on or before March 11, 1994, will 
be considered in the preparation of the final rule. Public Hearings 
will be held during the week of February 21, 1994, in Fresno, 
Sacramento, and San Francisco, California.

ADDRESSES: Written comments should be addressed to Patrick Wright, Bay/
Delta Program Manager, Water Quality Standards Branch, W-3, Water 
Management Division, Environmental Protection Agency, 75 Hawthorne 
Street, San Francisco, California 94105.
    Both oral and written comments will be accepted at the hearings. 
EPA reserves the right to fix reasonable limits on the time allowed for 
oral presentations. Written comments are encouraged.
    Contact Lois Grunwald, Public Affairs Office, Environmental 
Protection Agency, 75 Hawthorne Street, San Francisco, California 
94105, 415/744-1588, for further information on hearings.

FOR FURTHER INFORMATION CONTACT: Patrick Wright, Bay/Delta Program 
Manager, Water Quality Standards Branch, W-3, Water Management 
Division, Environmental Protection Agency, 75 Hawthorne Street, San 
Francisco, California 94105, 415/744-1993.

SUPPLEMENTARY INFORMATION: Section 303 of the Clean Water Act, as 
amended (hereinafter CWA or the Act), requires each state to adopt 
water quality standards consisting of designated uses and instream 
water quality criteria to protect such uses for all waters of the 
United States located within that state. Section 303(c) of the Act 
provides that states shall review and, if appropriate, revise the water 
quality standards at least once every three years. Any new or revised 
standards adopted by the state are to be reviewed and approved or 
disapproved by the U.S. Environmental Protection Agency (EPA or the 
Agency). In the event that EPA disapproves a state's standards, and the 
state does not make EPA's requested changes within ninety (90) days of 
the disapproval, or if EPA determines at any time that revised or new 
standards are necessary to meet the requirements of the Act, section 
303(c)(4) of the Act states that the Administrator shall promptly 
prepare and publish proposed regulations establishing water quality 
standards for the applicable waterbodies. The Administrator shall 
promulgate any new or revised standards not later than ninety (90) days 
after publication of the proposed standards. EPA's regulations for 
implementing section 303(c) of the Act are codified at 40 CFR part 131. 
Guidance for implementing these regulations is contained in the Water 
Quality Standards Handbook (December 1983) and Technical Support 
Manual: Waterbody Surveys and Assessments for Conducting Use 
Attainability Analyses (Volumes I, II and III).
    EPA's proposal is part of a coordinated federal interagency 
response to the water management issues in the San Francisco Bay and 
Delta. EPA has worked closely with the U.S. Fish and Wildlife Service 
(USFWS), the National Marine Fisheries Service (NMFS), and the U.S. 
Bureau of Reclamation (USBR) to develop a comprehensive, habitat-
oriented approach to water and fish and wildlife resource management 
issues in California. Other components of this interagency initiative 
are being announced contemporaneously with EPA's proposal. These 
include USFWS actions on petitions to list the longfin smelt and 
Sacramento splittail as endangered fish species under the Federal 
Endangered Species Act, 16 U.S.C. Secs. 1531 to 1540 (ESA), the USFWS 
proposal of critical habitat for the Delta smelt under the ESA, and the 
NMFS reclassification of the winter-run Chinook salmon as endangered 
under the ESA.

A. Background

    The San Francisco Bay/Sacramento-San Joaquin River Delta estuary 
(hereinafter the Bay/Delta) is the West Coast's largest estuary. It 
encompasses roughly 1600 square miles, and drains over 40 percent of 
California. The Bay/Delta is the point of convergence of California's 
two major river systems--the Sacramento River system flowing southward 
and draining a large part of northern California, and the San Joaquin 
River system flowing northward and draining a large part of central 
California. These two rivers, together with a number of smaller rivers 
flowing directly westward from the mountains, come together in a 
network of channels and islands, roughly a triangle 90 miles on each 
side, known as the Sacramento-San Joaquin Delta. The rivers converge at 
the western tip of the Delta, forming an estuary as fresh water mixes 
with marine water through a series of bays, channels, shoals and 
marshes and ultimately flowing into San Francisco Bay and then to the 
Pacific Ocean.
    The Bay/Delta constitutes one of the largest systems for fish 
production in the country, supplying habitat for over 120 fish species. 
It also comprises one of the largest areas of waterfowl habitat in the 
United States, providing a stopover for more than one-half of the 
waterfowl and shorebirds migrating on the Pacific Flyway. Within the 
boundaries of the Bay/Delta is the Suisun Marsh, the largest brackish 
marsh on the West Coast.
    The Bay/Delta is also the hub of California's two major water 
distribution systems--the Central Valley Project (CVP) built and 
operated by the USBR and the State of California's State Water Project 
(SWP). Most of the State's developed water--75 to 85 percent--is used 
for irrigation purposes by agriculture, irrigating over 4.5 million 
acres throughout the State. The Bay/Delta watershed also provides part 
or all of the drinking water supply for over 18 million people.
    Located solely within the State of California, the Bay/Delta is 
subject under state law to the water quality control jurisdiction of 
the California State Water Resources Control Board (State Board) and 
two regional boards, the Central Valley and San Francisco Regional 
Water Quality Control Boards. Under the California regulatory scheme, 
the State Board's actions preempt regional board actions to the extent 
of any conflicts. Cal. Water Code Sec. 13170.
    In 1978, the State Board adopted and submitted to EPA a Water 
Quality Control Plan (hereinafter the 1978 Delta Plan) containing a 
comprehensive set of water quality standards to protect the designated 
uses of the Bay/Delta. The 1978 Delta Plan included water quality 
standards for three categories of designated uses: municipal and 
industrial, agriculture, and fish and wildlife.1 The 1978 Delta 
Plan relied on a key set of criteria to protect fish and wildlife uses: 
the striped bass spawning and survival criteria. These criteria were 
established to provide minimum salinity and flow conditions to protect 
the fishery at levels that would have existed in the absence of the 
State and federal water projects (the so-called ``without projects'' 
level). The striped bass survival criteria were based on a statistical 
correlation between a Striped Bass Index (SBI) (a measure of the 
relative abundance of young striped bass in the estuary) and two 
hydrological variables: (1) Delta outflow (freshwater flowing through 
the Delta out to the ocean), and (2) Delta diversions (freshwater 
diverted out of the Delta channels for consumptive uses in agricultural 
irrigation, municipal and industrial uses). Based on this relationship, 
flow (measured in cubic feet per second (cfs) of Delta outflow) and 
salinity requirements at critical points in the Bay/Delta were adopted 
as criteria. The SBI, although not a formal criteria, was used to 
measure and predict the substantive environmental results of 
implementing these flow and salinity criteria. The 1978 Delta Plan 
emphasized striped bass protection because of the economic importance 
and availability of scientific information on this species in the Bay/
Delta, but the Plan also indicated that it considered the striped bass 
standards to be a surrogate for protection of other species.
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    \1\The CWA and implementing regulations describe the two 
components of water quality standards as ``designated uses'' and 
``water quality criteria'' (40 CFR 131.3(i)), whereas California 
uses the terms ``beneficial uses'' and ``objectives''. It has been 
EPA's and California's longstanding practice to interpret these 
terms synonymously. To avoid confusion, this proposal will use the 
federal terms ``designated uses'' and ``criteria''.
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    Pursuant to its obligations under section 303(c)(3) of the Act, EPA 
reviewed the 1978 Delta Plan in 1980. While EPA approved the Plan, it 
was concerned that the 1978 Delta Plan standards would not provide 
adequate protection of striped bass and the estuary's fishery 
resources. EPA therefore conditioned its approval upon a set of 
``interpretations'' of the standards, including commitments by the 
State Board to review and revise the 1978 Delta Plan standards 
immediately if there were measurable adverse impacts on striped bass 
spawning, or if necessary to attain ``without project'' levels of 
protection for the striped bass (as defined by an SBI value of 79). EPA 
also conditioned its approval on the State Board's commitment to 
develop additional criteria to protect aquatic life and tidal wetlands 
in and surrounding the Suisun Marsh. The State Board concurred with 
these interpretations in its letter to EPA dated November 21, 1980.
    In the years since the 1978 Delta Plan was adopted, these standards 
have not accomplished the intended goal of maintaining the SBI at a 
long term average of 79, the 1978 Delta Plan's estimate of ``without 
project'' levels. Indeed, during the 1980's, the SBI averaged 
approximately 7.5, and in 1983 and 1985 reached all-time lows of 1.2 
and 2.2. Some of the decline in the SBI may be attributable to drought 
conditions in the late 1970's and again in the late 1980's. However, 
the highest SBI values actually attained since the 1978 Delta Plan was 
adopted were only in the teens and 20's, a substantial shortfall from 
the stated goal of 79.
    The precipitous decline in striped bass is indicative of the poor 
health of other aquatic resources in the estuary. Several species have 
experienced similar declines, including chinook salmon (the winter-run 
of chinook salmon is listed as a threatened species under the ESA, and 
is currently proposed for reclassification as endangered), Delta smelt 
(recently listed as a threatened species under the ESA) and Sacramento 
splittail and longfin smelt (both the subject of a recent petition for 
listing as endangered species). The California Department of Fish and 
Game (California DFG) recently testified that virtually all of the 
estuary's major fish species are in clear decline. (CDFG 1992b, WRINT-
DFG-8)2
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    \2\If a reference was presented to the State Board during one of 
its hearings, this preamble will present citations in both the 
standard scientific form and in the State Board hearing record form. 
Accordingly, the eighth exhibit submitted by California DFG at the 
Board's interim water rights hearings in the summer of 1992 is cited 
as indicated.
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    As fishery resources continued to decline, EPA on several occasions 
expressed its concern to the State Board about the need for standards 
to adequately protect these resources. Throughout the first and second 
triennial reviews ending in 1981 and 1985, EPA urged the State Board to 
review and revise the 1978 Delta Plan in accordance with EPA's 1980 
approval letter. At the conclusion of each triennial review, the State 
Board made no changes.
    After its second triennial review, in a letter to EPA dated June 
23, 1986, the State Board acknowledged that the 1978 Delta Plan 
standards were not adequate to protect the estuary's fishery resources. 
It then outlined the hearing process it was planning for revising the 
standards. In response, and as part of its consideration of the State 
Board's second triennial review, EPA, on June 29, 1987, sent a letter 
to the State Board stating that EPA could no longer approve the striped 
bass survival standards (or the related provision allowing relaxation 
of the spawning standard in drier years) because these standards did 
not adequately protect the designated uses. EPA recognized, however, 
that the State Board had initiated new hearings to revise the 1978 
Delta Plan standards. EPA therefore indicated that it would await the 
results of the new hearings and approve or disapprove the revised 
standards after the State Board's submission to EPA of a complete set 
of revised standards.
    In addition to EPA's review under the CWA, the 1978 Delta Plan also 
received intense scrutiny under state law in California state court. 
This review culminated in a state appellate decision, United States, 
et. al. v. State Water Resources Control Board, 182 Cal. App. 2d 82 
(1st Dist., 1986) (known as the ``Racanelli Decision'' after its 
author, Judge John T. Racanelli). Among that decision's many holdings 
was the conclusion that the 1978 Delta Plan's water quality standards 
had been impermissibly limited to those standards that could be 
enforced against only the SWP and CVP (instead of against all water 
users). The court took notice that the State Board had proposed 
hearings to develop revisions to the 1978 Delta Plan, and asked the 
State Board to remedy the Plan's shortcomings in those hearings.
    Following the first phase of the new hearings, the State Board in 
November 1988 issued a draft Plan that included revised salinity and 
flow standards to protect the fisheries and other designated uses. The 
State Board subsequently withdrew that draft Plan, however, and issued 
a revised workplan that served as the basis for the State Board's 
present Water Quality Control Plan for Salinity for the San Francisco 
Bay/Sacramento-San Joaquin Delta Estuary (1991 Bay/Delta Plan).
    In accordance with the revised workplan, the State Board, on May 1, 
1991, adopted State Board Resolution No. 91-34, formally approving the 
1991 Bay/Delta Plan. The Plan restated the specific designated uses 
that had been included in the 1978 Delta Plan and related regional 
board basin plans. As restated, the designated uses included the 
following: Agricultural Supply, Cold and Warm Fresh-Water Habitat, 
Estuarine Habitat, Fish Migration, Fish Spawning, Groundwater Recharge, 
Industrial Process Supply, Industrial Service Supply, Municipal and 
Domestic Supply, Navigation, Contact and Non-Contact Water Recreation, 
Ocean Commercial and Sport Fishing, Preservation of Rare and Endangered 
Species, Shellfish Harvesting, and Wildlife Habitat.
    The 1991 Bay/Delta Plan, which was submitted for EPA's review on 
May 29, 1991, amended certain salinity criteria and adopted new 
temperature and dissolved oxygen criteria for specified locations in 
the estuary. The changes to the criteria, however, were of minimal 
substance. The 1991 Bay/Delta Plan did not revise the earlier 1978 
Delta Plan to address EPA's longstanding concerns about adequate 
protection for the designated fish and wildlife uses of the Bay/Delta.
    On September 3, 1991, EPA approved in part and disapproved in part 
the provisions of the 1991 Bay/Delta Plan. EPA's letter found that 
``[t]he record * * * does not support the conclusion that the State has 
adopted criteria sufficient to protect the designated uses'' of the 
estuary. The designated uses at risk, as defined by the State Board, 
include Estuarine Habitat, and also Cold and Warm Water Habitat, Fish 
Migration, Fish Spawning, Ocean Commercial and Sport Fishing, 
Preservation of Rare and Endangered Species, Shellfish Harvesting, and 
Wildlife Habitat. In addition to its general finding that the 1991 Bay/
Delta Plan did not contain sufficient criteria to protect the 
designated uses, EPA also disapproved the absence of salinity standards 
to protect fish and wildlife uses in the Suisun, San Pablo, and San 
Francisco Bays and Suisun Marsh, the absence of scientifically 
supportable salinity standards (measured by electrical conductivity) to 
protect the Fish Spawning uses of the lower San Joaquin River, and the 
absence of scientifically supportable temperature standards on the San 
Joaquin and Sacramento Rivers to protect the fall-run and winter-run 
chinook salmon.
    Pursuant to section 303(c)(3) of the Act, the State Board had 90 
days to make changes to the criteria disapproved by EPA in its 
September 3, 1991 letter. The State Board made no such revisions during 
the 90 day period or at any subsequent time. However, in the summer of 
1992, the State Board, at the request of the Governor of the State of 
California, held hearings for the purpose of establishing interim 
measures to protect the natural resources in the Bay/Delta estuary. In 
keeping with the CWA's recognition that the states have primary 
responsibility for setting water quality standards, EPA participated in 
these hearings--rather than proposing federal standards at that time--
in the hope that the hearings would result in state adoption of 
approvable standards and preclude the need for a federal rulemaking. 
EPA submitted opening and closing statements to the State Board, and 
joined with NMFS and USFWS in submitting an Interagency Statement of 
Principles. These statements recommended that the State Board adopt a 
habitat and ecosystem-based approach to standards that would satisfy 
CWA requirements and meet the State Board's goal of reversing the 
decline of the estuary's fish and wildlife resources.
    At the conclusion of these hearings, the State Board, on December 
10, 1992, issued its recommended interim measures in Draft Water Rights 
Decision (hereinafter D-1630). The Draft contained new water export 
limits and pumping restrictions and ordered ``pulse flows'' to help 
transport young migratory fish through the Delta. It also imposed water 
conservation measures on agricultural and urban users, and established 
a restoration fund financed by user fees to pay for conservation 
efforts in the Bay/Delta. Although D-1630 proposed several changes in 
the operation of the water facilities affecting the estuary that would 
be beneficial to its natural resources, EPA informed the State Board in 
its comments dated January 13, 1993, that D-1630, if adopted, would not 
satisfy the requirements of the Act. EPA noted that D-1630, a proposed 
water rights decision, did not purport to revise the State's water 
quality standards at all, and therefore did not affect EPA's prior 
decision disapproving the 1991 Bay/Delta Plan. Moreover, EPA noted that 
the measures in D-1630 were not tied to specific designated uses in the 
estuary (including the Estuarine Habitat, Fish Spawning, and 
Preservation of Rare and Endangered Species uses), and that no attempt 
had been made to assure that the designated uses would be protected. 
Accordingly, EPA found that D-1630 ``meets neither the procedural nor 
the substantive requirements of the Clean Water Act.'' After the close 
of the comment period for D-1630, the State Board, in response to a 
subsequent request by the Governor, declined to adopt D-1630.
    In response to the State Board's failure to revise the criteria 
disapproved in EPA's September 3, 1991 letter, EPA, pursuant to section 
303 (c)(3) and (c)(4) of the Act, is proposing regulations establishing 
revised water quality criteria which would in effect supersede and 
supplement the disapproved State criteria for purposes of the CWA.

B. Statutory Basis and Purpose

    Section 303(c) of the Act requires that state water quality 
standards ``* * * be such as to protect the public health or welfare, 
enhance the quality of water and serve the purposes of this Act. Such 
standards shall be established taking into consideration their use and 
value for propagation of fish and wildlife. * * *'' Key concerns of 
this statutory provision are the enhancement of water quality and the 
protection of the propagation of fish. The ultimate purpose of water 
quality standards, as with the other sections of the Act, is to restore 
and maintain the chemical, physical, and biological integrity of the 
Nation's waters. CWA section 101(a).
    Under section 303(c) of the Act, a water quality standard for a 
specific waterbody consists of two components: a designated use for 
which a waterbody is to be protected (such as recreation, fish and 
wildlife, or agriculture) and a numerical or qualitative water quality 
criterion which supports the designated use.
    The Act gives primary responsibility for the adoption of water 
quality standards to the states. After adopting its initial water 
quality standards, a state is required, no less than every three years, 
to review those standards and, if necessary, modify them. Under section 
303(c)(1) of the Act, the results of these triennial reviews are to be 
submitted to EPA for review and approval or disapproval.
    EPA's Water Quality Standards regulations at 40 CFR part 131 
specify the requirements for water quality criteria. States must adopt 
those water quality criteria that protect the designated use. Such 
criteria must be based on sound scientific rationale and must contain 
sufficient parameters or constituents to protect the designated use. 
For waters with multiple use designations, the criteria shall support 
the most sensitive use. (see 40 CFR 131.11(a).
    In addition, a state's criteria must be consistent with the state's 
antidegradation policy. The federal regulations provide that, at a 
minimum, the state must maintain ``[e]xisting instream water uses 
[those existing in the waterbody at any time on or after November 28, 
1975] and the level of water quality necessary to protect the existing 
uses. * * *'' 40 CFR 131.12(a)(1). In order to approve a state's water 
quality criteria, EPA must determine whether the state has adopted 
``water quality criteria [that are] sufficient to protect the 
designated uses.'' 40 CFR 131.6(c).
    Section 303(c)(4) of the Act provides that the Administrator shall 
promptly prepare and publish proposed regulations establishing a new or 
revised standard in either of two situations: First, when the 
Administrator has disapproved a state standard under section 303(c)(3) 
and the state has not taken corrective action within 90 days; and, 
second, in any case where the Administrator determines that a revised 
or new standard is necessary to meet the requirements of the Act. Once 
promulgated, the federal regulations are applicable to the state's 
waters, and, if they are more stringent, have the effect of supplanting 
and supplementing the state's standards. However, it is EPA's 
longstanding policy that the federal regulations will be withdrawn if a 
state adopts and submits standards that in the Agency's judgment meet 
the requirements of the Act.
    In reviewing California's implementation of its water quality 
standards program, EPA has considered the provisions of section 101(g) 
of the Act, which restate the long-standing policy of Federal deference 
to state water allocation functions: ``It is the policy of Congress 
that the authority of each State to allocate quantities of water within 
its jurisdiction shall not be superseded, abrogated or otherwise 
impaired by this [Act].'' The General Counsel of EPA, in a Memorandum 
to Regional Administrators dated November 7, 1978, interpreted this 
statutory provision in the context of the water quality standards 
program and concluded that ``EPA should therefore impose requirements 
which affect water usage only where they are clearly necessary to meet 
the Act's requirements.'' See also Memorandum from Robert M. Perry, 
General Counsel, to Frederic A. Eidsness, Jr., Assistant Administrator 
for Water, dated March 17, 1983 (considering interplay of section 
101(g) and the guidelines under section 404(b)(1) of the Act). These 
positions of the General Counsel are consistent with the existing 
judicial precedent interpreting section 101(g). The leading case 
interpreting section 101(g) in light of the other mandates of the CWA, 
Riverside Irrigation Dist. v. Andrews, 758 F.2d 508, 513 (10th Cir. 
1985), held that section 101(g) is only a general policy statement 
which ``cannot nullify a clear and specific grant of jurisdiction.'' 
Id. at 513. The Court then examined the legislative history of the Act 
and concluded that ``where both the state's interest in allocating 
water and the federal government's interest in protecting the 
environment are implicated, Congress intended an accommodation.'' Id. 
See also United States v. Akers, 785 F.2d 814 (9th Cir. 1986) (adopting 
Riverside in the 9th Circuit on similar facts).
    As the discussion above indicates, EPA has attempted to accommodate 
the State Board processes procedurally, generally deferring to the 
State Board schedules for review and revision of its water quality 
standards, even though this State process has continued for almost a 
decade and has frequently exceeded the Act's required triennial review 
requirements. Similarly, EPA is in this proposal attempting to 
accommodate the State's interest substantively. Although the State 
Board, in the 1978 Delta Plan, adopted explicit flow criteria, EPA is 
refraining from proposing direct revisions to the flow criteria. 
Instead, EPA is proposing criteria that describe the habitat conditions 
necessary to protect the designated uses of the Bay/Delta. The State 
Board still has full discretion to develop implementation measures 
attaining those habitat conditions, and still retains full discretion 
over the allocation of water necessary to achieve the criteria. 
Finally, EPA has fully considered the record developed in the State 
Board's 1992 hearings on D-1630 and, to the extent possible, has 
incorporated the scientific information presented in those hearings in 
the proposed criteria.
    The State Board's adoption of the 1978 Delta Plan, and of the 
revised Bay/Delta Plan in 1991, were intended to meet the State's 
obligations to establish water quality standards under the CWA. 
Pursuant to its mandate under section 303(c)(3) of the Act, on 
September 3, 1991, EPA disapproved several of the criteria contained in 
the State Board's plan. For the reasons outlined herein and in EPA's 
letter of September 3, 1991, the Administrator finds that the water 
quality criteria adopted by the State fail to protect the designated 
uses and the criteria proposed below would meet the requirements of the 
Act. Accordingly, pursuant to sections 303(c)(3) and 303(c)(4) of the 
Act, the Administrator is proposing the following water quality 
criteria applicable to California waters.

C. Proposed Criteria

    EPA is proposing three different sets of water quality criteria: 
Salinity criteria protecting estuarine habitat in the Suisun Bay area, 
salmon smolt survival indices protecting salmon migration, and an 
electrical conductivity criterion protecting striped bass spawning on 
the lower San Joaquin River. Each set of criteria is intended to 
protect a particular designated use or set of uses in the Bay/Delta 
estuary. As discussed above, these designated uses were originally 
established by the regional boards in the individual basin plans and by 
the State Board in its 1978 Delta Plan, and were reaffirmed and 
restated in the 1991 Bay/Delta Plan. The discussion below describes 
each set of proposed criteria in detail and outlines the scientific 
basis for the proposals.
    In developing these proposed criteria, EPA has considered the 
scientific evidence and testimony presented during the State Board's 
1992 hearing process, as well as scientific information from other 
sources. In particular, EPA has relied upon the recommendations of the 
USFWS, of Dr. Peter Moyle, Professor in the Department of Wildlife and 
Fisheries Biology at the University of California at Davis and author 
of more than 100 articles and books on the ecology of the inland fishes 
of California, and of a distinguished panel of scientists who 
participated in a series of workshops sponsored by the San Francisco 
Estuary Project (SFEP).
    EPA's proposed criteria are consistent with the Interagency 
Statement of Principles dated June 15, 1992 and submitted to the State 
Board by EPA, USFWS, and NMFS during the Board's 1992 hearings. This 
Interagency Statement recommended that the State Board develop a 
comprehensive habitat protection approach to restore and maintain the 
ecological health of the estuary, and provided a framework for both 
interim and long-term standards. The Interagency Statement also 
emphasized that there is a consensus among the three federal agencies 
that the existing scientific information is sufficient to set criteria 
to protect the designated uses of the estuary.
    The criteria proposed below are similar to those EPA has outlined 
in letters and statements to State and federal agencies, including in 
the following: its September 3, 1991 disapproval letter to the State 
Board; its June 11, 1992 policy statement and its August 24, 1992 
closing statement submitted to the State Board's 1992 hearings; and its 
October 29, 1992 letter to USFWS and NMFS. Throughout this process, EPA 
has carefully coordinated its actions and proposals with other State 
and Federal environmental agencies to achieve a consensus on the water 
quality criteria necessary to protect the estuary.

1. Estuarine Habitat Criteria

a. Designated Uses and EPA's Disapproval
    The State's 1991 Bay/Delta Plan included ``Estuarine Habitat'' as a 
designated use for the Bay/Delta estuary. As described more fully in 
the Water Quality Control Plan, San Francisco Bay Basin [2], December 
1986, at II-4, this Estuarine Habitat designated use is intended to 
provide ``an essential and unique habitat that serves to acclimate 
anadromous fishes (salmon, striped bass) migrating into fresh or marine 
conditions. This habitat also provides for the propagation and 
sustenance of a variety of fish and shellfish, numerous waterfowl and 
shore birds, and marine mammals.'' Related fish and wildlife uses of 
the Bay/Delta estuary designated by the State Board include Ocean 
Commercial and Sport Fishing, Preservation of Rare and Endangered 
Species, Shellfish Harvesting, Fish Migration, and Wildlife Habitat. To 
protect these designated uses, the 1991 Bay/Delta Plan included 
dissolved oxygen and temperature criteria to protect chinook salmon, 
outflow and salinity criteria to protect striped bass, and salinity 
criteria to protect the managed (non-tidal) areas of Suisun Marsh.
    Unfortunately, the specific criteria adopted by the State Board 
clearly do not protect the integrity of the Estuarine Habitat 
designated use. Although EPA had already many times noted the 
inadequacies of the 1978 Delta Plan, the 1991 Bay/Delta Plan made only 
minor adjustments to criteria protecting striped bass, salmon, and the 
managed portions of the Suisun Marsh, and provided no criteria 
specifically addressing the Estuarine Habitat designated use.
    The shortcomings of the State Board's criteria are reflected by the 
continued deterioration of the estuary's resources. The SBI, used as a 
measure of the health of the 1978 Delta Plan's indicator species, has 
never attained its targeted value of 79, and instead has plummeted to 
unprecedented low values. Recent testimony by the California DFG 
indicates that virtually all of the estuary's major fish species are in 
clear decline (CDFG 1992b, WRINT-DFG-8). As noted above in the 
recitation of the history of the Bay/Delta, many species relying on the 
estuarine habitat are listed or are being considered for listing under 
the ESA. One recent report suggests that at least five of the estuary's 
fish species (longfin smelt, spring-run Chinook salmon, Sacramento 
splittail, green sturgeon, and Red Hills roach) qualify for immediate 
listing under the ESA (Moyle and Yoshiyama 1992), in addition to the 
already listed winter-run Chinook salmon and Delta smelt.
    California's Gov. Wilson highlighted the seriousness of the 
problems in the Bay/Delta when he announced his new water policy on 
April 6, 1992.

    California has many species with populations in serious decline, 
and some faced with extinction. Both existing and proposed water 
projects often have an impact upon protected animal and plant 
species. * * *
* * * * *
    [A]ny program must begin by recognizing a disturbing truth: The 
Delta is broken.

    Gov. Wilson also outlined the kinds of measures necessary to 
protect the Bay/Delta: ``If we are to be good stewards of our fish and 
wildlife, we must begin to mitigate these impacts by providing larger 
streamflows, greater Delta outflow, restoration of spawning gravel and 
provision of fish screens and temperature control measures.'' In 
response to Gov. Wilson's proposal, the State Board initiated the D-
1630 process, the ``immediate goal'' of which was ``to halt the decline 
and increase the protection of public trust resources where 
reasonable.'' (SWRCB 1992b). However, as explained above, California 
abandoned the D-1630 process, and the State Board has yet to develop 
criteria that adequately protect the Estuarine Habitat designated use.
    In its disapproval letter of September 3, 1991, EPA formally found 
that the set of water quality criteria adopted by the State Board in 
the 1991 Bay/Delta Plan failed to protect the Estuarine Habitat and 
other designated fish and wildlife uses of the estuary.

    To be consistent with the Clean Water Act and the accompanying 
Regulations, the State's [criteria] must be sufficient to protect 
Estuarine Habitat and other designated fish and wildlife uses. The 
Estuarine Habitat use, which has been formally approved by the State 
and EPA as part of the State's water quality standards, was 
established to provide ``an essential and unique habitat that serves 
to acclimate anadromous fishes (salmon, striped bass) migrating into 
fresh or marine conditions. This habitat also provides for the 
propagation and sustenance of a variety of fish and shellfish, 
numerous waterfowl and shore birds, and marine mammals. Water 
Quality Control Plan, San Francisco Bay Basin(2), December 1986, at 
II-4.
* * * * *
* * * * *
    The record * * *  does not support the conclusion that the State 
has adopted criteria sufficient to protect the designated uses. 
Accordingly * * *  I hereby disapprove the current set of [criteria] 
contained in the State Board's Bay/Delta Plan because they fail to 
protect the Estuarine Habitat and the other designated fish and 
wildlife uses of the estuary.

    Given the State Board's failure to address EPA's concerns either 
directly or in the D-1630 process, EPA is proposing to supplement the 
State's criteria with additional salinity criteria to protect the 
Estuarine Habitat designated use and related fish and wildlife uses of 
the estuary described above. EPA is emphasizing the Estuarine Habitat 
designated use because of its importance to the whole spectrum of fish 
and wildlife uses in the estuary. This emphasis is consistent with the 
Interagency Statement of Principles' recommendation that restoration 
efforts focus on habitat protection. The discussion below describes the 
scientific basis for salinity criteria and presents EPA's conclusions 
as to this proposal.
b. Developing Salinity Criteria
    In developing proposed criteria protecting Estuarine Habitat, EPA 
has considered the complex hydrological and biological nature of the 
Bay/Delta estuarine system. Habitat conditions in the estuary change 
from month to month and year to year primarily in response to 
precipitation upstream, reservoir operations, agricultural patterns and 
export rates (Nichols et al. 1986). Many important environmental 
characteristics within the Delta and Bay respond to changes in water 
availability, storage and use. The environmental characteristics of 
particular biological importance include flow rates and volumes within 
river channels and the Bay, salinity and turbidity levels, water 
temperature, and the degree of stratification of the water column. 
Correlations among all these variables are high; thus, each is often a 
good indicator of the other. However, other factors such as wind, tidal 
stage, and antecedent conditions influence the day to day values of 
each variable.
    When EPA disapproved the State's criteria on September 3, 1991, it 
suggested that the State could develop approvable replacement criteria 
using a number of alternative methodologies: it could adopt additional 
salinity and temperature criteria, adopt revised flow criteria, adopt 
biological criteria, or develop a combination of these or other 
scientifically-defensible criteria protecting the designated Estuarine 
Habitat and fish and wildlife uses in the estuary. Upon the State's 
failure to revise its criteria during the statutory 90 day period (or 
during the D-1630 process), EPA began developing a federal proposal for 
criteria protecting the applicable designated uses.
    (1) Entrapment Zone. The ``entrapment zone'' was the focus of EPA's 
initial consideration of water quality criteria due primarily to its 
perceived importance to the food chain. The entrapment zone, where 
ocean water flowing landward at depth mixes with freshwater flowing 
seaward at the surface (Kimmerer 1992), is widely acknowledged to be 
one of the most important habitats within the estuary. Salinities are 
usually between 2 and 10 ppt, turbidity and phytoplankton densities are 
high, and young fish of several species are most abundant in this zone. 
One of the most important aspects of the entrapment zone is the 
localized high density of prey. The closest association of predator and 
prey with the entrapment zone is shown by Delta smelt and its principal 
food item, the copepod Eurytemora affinis (Moyle et al. 1992). 
Similarly, young striped bass and their principal food item, the shrimp 
Neomysis affinis, are found in the greatest abundance in salinities 
between 2 and 10 ppt. (Heubach 1969, Siegfried et al. 1979, Orsi and 
Knutson 1979, Knutson and Orsi 1983, Orsi and Mecum 1986, Obrebski, et 
al. 1992). Many young fish require high food densities in order to 
obtain sufficient food for growth (Moyle and Cech 1988), and it has 
been suggested that the density of food in the entrapment zone may 
affect fish survival and abundance. However, no direct evidence of 
starvation has been demonstrated for the declining fish populations of 
the estuary (Bennett et al. 1990, Moyle et al. 1992). The location of 
the entrapment zone has also been shown to be important for organisms 
at lower trophic levels (that is, organisms that are lower on the food 
chain). Phytoplankton densities are higher when the entrapment zone is 
within the relatively-shallow Suisun Bay than when it is further 
upstream in deeper channels (Arthur and Ball 1980). Measurements of 
phytoplankton growth rates show that shallow areas are ten times as 
productive as channel areas (Cloern et al. 1983).
    In large part because of the relationship between fishery 
productivity and the entrapment zone described above, EPA initially 
considered developing federal criteria designed to directly maintain 
and protect the entrapment zone. However, as described below, 
discussions among the participants in a workshop convened by the SFEP 
suggested that salinity criteria would be a more appropriate measure 
for protecting estuarine habitat.
    (2) San Francisco Estuary Project Workshop Findings. The SFEP is a 
five-year cooperative effort by over 100 representatives of public and 
private entities concerned about the water quality and natural 
resources of the San Francisco Bay estuary. Funded primarily by EPA and 
the State of California, the SFEP has developed a Comprehensive 
Conservation and Management Plan to protect the natural and consumptive 
water uses of the Bay/Delta (SFEP 1993a). In 1991 and 1992, the SFEP 
convened a series of workshops to develop the scientific rationale for 
an estuarine index that would measure the responses of estuarine biota 
and habitats to various conditions of salinity and flow. The workshops 
involved approximately thirty scientists and policy makers with 
expertise in estuarine ecology and water resource management, and 
included several of the world's most distinguished estuarine 
scientists. The group focused its attention on the estuary between 
Carquinez Strait and the confluence of the Sacramento and San Joaquin 
Rivers. The specific operations of the water projects (water exports, 
gate closures, etc.) were not directly addressed by the group.
    The findings of the workshops were assembled in a final report, 
Managing Freshwater Discharge to the San Francisco Bay/Sacramento-San 
Joaquin Delta Estuary: The Scientific Basis for an Estuarine Standard 
(SFEP 1993b) (SFEP Report). All of the conclusions and recommendations 
in this report were endorsed by a consensus of the estuarine scientists 
and managers who participated in the final workshop in August of 
1992.3
---------------------------------------------------------------------------

    \3\The SFEP Report defined ``consensus'' as follows: ``The term 
consensus is used to represent group solidarity on an issue; a 
judgement arrived at by most of the scientists and managers present. 
In all cases, the consensus was unanimous or nearly unanimous.'' 
SFEP Report, at p. 3. EPA recognizes that representatives from a 
number of the participating organizations (the State Water 
Contractors, the California Department of Water Resources 
(California DWR), the State Board, and the USBR) subsequently 
withdrew their names from the final SFEP Report. According to the 
Final Report, the conclusions are based on the consensus that was 
achieved by the participants at the workshops.
---------------------------------------------------------------------------

    Although the workshop group initially focused on the entrapment 
zone, they concluded that salinity would be a more appropriate index 
for the development of estuarine standards. Salinity was selected for 
several reasons: It is of direct ecological importance, it can be 
measured accurately and easily, and it integrates a number of important 
estuarine properties and processes. In particular, it is closely 
associated with the abundance and distribution of species at all 
trophic levels (SFEP 1993b). The workgroup further concluded that the 
placement of the 2 parts per thousand isohaline\4\ should be used to 
develop estuarine standards.
---------------------------------------------------------------------------

    \4\An ``isohaline'' is defined as a theoretical or imaginary 
line in the estuary connecting all points of equal salinity. For 
example, the phrase ``2 near-bottom isohaline'' means a 
line stretching across the Delta marking the positions where the 
salinity of the near-bottom water is 2 parts per thousand. The 
position of an isohaline in an estuary changes dramatically during 
the day because of rising and falling tides, which sometimes move 
the isohaline as much as 5 miles up or downstream during a 24 hour 
period. By convention, a daily isohaline is measured at its daily 
mean position for the 24 hour period.
---------------------------------------------------------------------------

    Because of the broad spectrum of scientific expertise underlying 
the SFEP Report, its conclusions and recommendations are included in 
full as appendix I. For purposes of developing water quality criteria 
protecting Estuarine Habitat, the following conclusions and 
recommendations are especially relevant:

* * * * *

(2) Conclusion

    Estuarine standards to be used in conjunction with flow 
standards should be based upon an index that is simple and 
inexpensive to measure accurately, that has ecological significance, 
that integrates a number of important estuarine properties and 
processes, and that is meaningful to a large number of 
constituencies.

Recommendation

    Salinity should be used as an index for the development of some 
estuarine standards.

(3) Conclusion

    Salinity measured at about 1m above the bottom5 is an index 
upon which estuarine standards should be developed. The index is a 
practical way of tracking changes in habitat.
---------------------------------------------------------------------------

    \5\Because the difference between surface and near-bottom 
salinities is small and because the relationship between them is 
reasonably well known, surface salinity could also be used. Near-
bottom salinity is recommended, however, because it is a more stable 
indicator. [Footnote in the original.]
---------------------------------------------------------------------------

Recommendation

    Standards should be developed using an index that establishes an 
upstream limit of the position of the 2 near-bottom 
isohaline, averaged over different periods of the year.
* * * * *

(7) Conclusion

    The position of the near-bottom 2 salinity isohaline 
is an index of habitat conditions for estuarine resources at all 
trophic levels, including the supply of organic matter to the food 
web of Suisun Bay, an important nursery area. In other words, well-
behaved statistical relationships exist between the near-bottom 
2 isohaline and many estuarine resources for which 
sufficient data exist to make appropriate analyses. Moreover, at 
least a rudimentary understanding exists for the causal mechanisms 
underlying many of these relationships. The location of the near-
bottom 2 isohaline is important either because it is a 
direct causal factor or because it is highly correlated with a 
direct causal factor (e.g., diversions).
    Preliminary analyses show that errors in prediction using models 
which incorporate only the position of the 2 isohaline are 
comparable to the errors using more complex models which incorporate 
additional flow-related variables. In other words, given the present 
data sets, predictive models using only the position of the near-
bottom 2 isohaline perform as well as more complex models 
that incorporate other variables. However, some of these other 
variables may be very important in affecting habitat and the 
condition of biological resources of the estuary.

Recommendations

    At this time, the most appropriate basis for setting salinity 
standards for the portion of the estuary on which this report 
concentrates is the position of the near-bottom 2 
isohaline alone, unless it can be shown either that another variable 
is the controlling variable or that incorporation of additional 
variables improves the predictive capability.
* * * * *

(10) Conclusion

    The actual setting of salinity standards--specifying the 
upstream locations of the near-bottom 2 isohaline for 
different periods of the year--should be keyed to environmental 
goals: to achieving and sustaining some desired biological response 
level specified in terms of habitat protection or abundance and 
survival rates of important and diagnostic estuarine and wetland 
species.

Recommendations

    Goals should be expressed in terms of desired conditions for 
some future time. Progress toward those goals should be monitored 
and reported widely. Environmental goals for the estuary will be 
most effective if they are expressed in terms of restoring 
conditions to those that existed at specific historical times. . . .

    In developing these conclusions, the workshop participants relied 
in part on a series of papers developed by Dr. Alan Jassby of the 
University of California at Davis and Dr. Wim Kimmerer of BioSystems 
Analysis, Inc. These papers concluded that the position of the 2 ppt 
isohaline is closely associated with the abundance of estuarine 
organisms at all trophic levels, as well as with the supply of organic 
matter from phytoplankton production and riverine loading 
(phytoplankton POC). The estuarine organisms include primary and 
secondary zooplankton consumers (Neomysis and Crangon), a major group 
of benthic consumers in Suisun Bay (mollusks), bottom-foraging fish 
(starry flounder), and both survival (striped bass) and abundance 
(striped bass and longfin smelt) of fish that feed in the water column. 
For each of these organisms, with the exception of mollusks, abundance 
levels increase as the position of the 2 ppt isohaline is located 
farther downstream (Jassby 1993).
    The SFEP's final report cautioned that these correlations are 
not proof of cause and effect relationships. That is, the report did 
not attempt to identify the causal mechanism linking the salinity 
regime and the abundance of estuarine organisms. Further, the report 
did not address other factors unrelated to water quality, such as 
overfishing, that may also have an impact on abundance of certain 
aquatic resources. Nevertheless, salinity integrates a number of 
important estuarine properties, is easy to measure, and is readily 
understood by all interested parties. The particular value of 2 ppt 
near-bottom salinity was selected because it occurs near the 
upstream limit of marine salt penetration, is higher than salinities 
derived from agricultural runoff, is close to the entrapment zone 
and is associated with little stratification of the water column. 
The group concluded that the location of the 2 ppt isohaline, 
measured as kilometers upstream from the Golden Gate Bridge, is the 
most appropriate index of habitat conditions underlying the 
variability in biological resources (SFEP 1993b).
    These findings in the SFEP workshop reports are entirely 
consistent with other scientific work in the Bay/Delta. For example, 
Dr. Peter Moyle testified to the State Board that nursery habitat 
(represented by areas of low salinity) in Suisun Bay is now more 
important than it was historically due to the high risks of 
entrainment6 faced by fishes in the Delta. After discussing a 
variety of mechanisms that may be behind the declines of most 
aquatic populations of the upper estuary, Dr. Moyle concluded that 
``[w]hile the exact mechanisms that account for the importance of 
having the [entrapment] zone in Suisun Bay (increased food supplies, 
physical concentration of organisms, association with higher flows, 
etc.) are being debated, there seems little doubt that many fish 
species depend on this location for their long-term survival'' 
(Moyle 1992, WRINT-NHI-9). Dr. Moyle recommended that in wetter 
years the zone of low salinity habitat should be located near Roe 
Island but that in drier years this requirement could be shifted 
upstream to Chipps Island. In addition, the USFWS cited the 
importance of low-salinity habitat in Suisun Bay in the January to 
June period in its 1991 proposal to designate critical habitat for 
Delta smelt under the ESA. 56 FR 50075 (October 3, 1991).
---------------------------------------------------------------------------

    \6\Strictly defined, ``entrainment'' is the displacement of fish 
or other aquatic organisms from their location in one waterbody to 
another as a result of the operation of a water diversion. In the 
Bay/Delta, however, the term ``entrainment'' is generally used to 
refer to the destruction of fish or larvae at the intake mechanisms 
of the many water diversion facilities in the Delta. Most 
entrainment occurs when fish or larvae are pulled into screens or 
pumps by the diversion apparatus.
---------------------------------------------------------------------------

c. Ecological Significance of Salinity Levels
    EPA is selecting the 2 ppt isohaline as the basis for its proposed 
criteria in part because that isohaline incorporates a whole range of 
factors relevant to the estuary's health, even though the operation of 
some of these factors is not fully understood. Some species that show 
high correlations with the location of the 2 ppt isohaline are not 
abundant in low salinity habitat and are probably responding to river 
flow or other correlated factors. However, salinity in the 2 ppt range 
is clearly and directly important to a broad range of estuarine species 
and the location of this salinity is strongly associated with the 
abundance and distribution of many of these species. The SFEP Report 
emphasized that it is well established scientifically that salinity has 
direct ecological importance to many estuarine species in this estuary 
and others throughout the world (SFEP 1993b). In fact, much of the 
distribution of estuarine species can be explained by their association 
with specific salinity ranges and their ability to survive and 
reproduce within certain salinity limits. The following sections 
summarize the best available evidence on the direct effects of the 
location of low salinity habitat on the distribution and abundance of 
key species and habitats within the Bay/Delta estuary. This scientific 
evidence provides substantial support for the need for the proposed 
salinity criteria protecting the water quality necessary to sustain the 
ecological health of the estuary.
    --Delta smelt. Delta smelt (Hypomesus transpacificus) are found 
today only in the upper reaches of the Sacramento-San Joaquin estuary. 
Early studies by the California DFG of the two most abundant smelts, 
longfin smelt and Delta smelt, noted that changes in the historical 
location of the entrapment zone would threaten populations of both 
species (Broadway 1979). In its initial notice of petition findings for 
the listing of the Delta smelt as threatened under the ESA, the USFWS 
found that ``the annual export of 6 million acre-feet of water by 
Federal, State and private agencies has allowed the intrusion of higher 
salinity seawater to the marshes. Because of higher salinities, the 
Delta smelt has lost spawning and nursery areas in Suisun Bay and 
Suisun Marsh.'' 55 FR 52852, 52853 (December 24, 1990). The final rule 
listing Delta smelt as a threatened species found that embryonic, 
larval and post-larval mortality rates increase as salinities in the 
western Delta increase and the entrapment zone moves upstream. Delta 
smelt larvae survive and grow best when the entrapment zone occupies a 
broad geographic area with extensive shallow areas. Delta smelt 
reproduction has probably suffered in recent years because the 
entrapment zone has been located east of Suisun Bay. 58 FR 12854 (March 
5, 1993).
    In the proposal to list the Delta smelt as a threatened species, 
the USFWS identified critical habitat for the species as requiring 
salinities less than 2 ppt in Suisun Bay from January through June. 56 
FR 50075, 50079 (October 3, 1991). When listing the Delta smelt as 
threatened, the USFWS deferred designation of critical habitat until 
October 1993. In summarizing the factors affecting Delta smelt, the 
USFWS concluded that the biological characteristics of the species made 
it very sensitive to perturbations in its reproductive habitat and 
larval nursery grounds. The final listing notice further determined 
that Suisun Bay is the primary nursery habitat for this species and 
that the habitat has been degraded because of higher salinities in the 
spring due to upstream freshwater diversions. 58 FR 12854, 12860 (March 
5, 1993).
    The USFWS's conclusions were also supported by an interagency Delta 
smelt working group convened by the USFWS after its proposal to list 
the species under the ESA. The working group included representatives 
of USFWS, EPA, USBR, California DFG, and the California DWR. The 
working group developed several recommendations to increase abundance 
levels of Delta smelt, including maintaining the 2 ppt zone in Suisun 
Bay during the Delta smelt's early months of life. The working group's 
recommendation was that low salinity habitat be kept in Suisun Bay in 
all years; no attempt was made to adjust the position of the zone to 
account for dry year conditions (USFWS 1992f, WRINT-USFWS-15).
    The USFWS's proposed critical habitat designation has been 
supported by a recently published paper by biologists of the California 
DFG and the University of California at Davis. The authors concluded 
that Delta smelt are most abundant in low salinity water associated 
with the entrapment zone. During the years preceding their decline, 
Delta smelt were found most abundantly at sites where low salinity 
conditions coincided with shallow habitats. Since their decline, low 
salinity conditions have been found in areas where little shallow 
habitat is available. The principal conclusion of these authors was 
that ``[r]estoration of the Delta smelt to a sustainable population 
size is likely to require maintenance of the [entrapment] zone in 
Suisun Bay and maintenance of net seaward flows in the lower San 
Joaquin River during the period when larvae are present'' (Moyle et al. 
1992).
    The State Board's 1991 Bay/Delta Plan also acknowledged that the 
location of the 2 ppt isohaline is important for Delta smelt, finding 
that ``existing knowledge suggests that salinities of 2 ppt or less are 
desired in Suisun Bay from March through June.'' However, rather than 
adopting protective salinity criteria, the State Board suggested that 
protection of low-salinity habitat would be dealt with as a ``flow'' 
issue in the subsequent scoping and water rights phases of its 
proceedings (1991 Bay/Delta Plan, p. 5-44). As explained in more detail 
above, to date the State Board has failed to adopt any additional 
standards since its 1991 Bay/Delta Plan.
    --Striped Bass. Striped bass (Morone saxatilis) support one of the 
most economically important sportfisheries in the Bay/Delta estuary. 
The striped bass population (and consequently the number of anglers) 
has plummeted since the early 1970's, with populations declining by as 
much as 70 percent from historical levels (Stevens et al. 1985; White 
1986; CDFG 1992b, WRINT-DFG-8). Although striped bass populations exist 
elsewhere in entirely freshwater habitats, the species thrives only in 
estuarine conditions (Talbot 1966), and in the Sacramento-San Joaquin 
estuary low salinity habitat appears to provide important nursery 
grounds (Wang 1986). Adult striped bass migrate upstream to spawn in 
fresh water. The planktonic larvae are carried downstream and 
concentrate in areas of low salinity (Moyle 1976). When this low 
salinity zone is located in Suisun Bay, survival of young bass is 
improved (Turner and Chadwick 1972). As a result, several parties have 
recommended that the entrapment zone be maintained in Suisun Bay to 
improve striped bass year class survival (Moyle 1992, WRINT-NHI-9; USBR 
1991, WRINT-USBR-2; USFWS 1992d, WRINT-USFWS-19; USFWS 1992e, WRINT-
USFWS-20; Moyle and Herbold 1989; Moyle, et al. 1989).
    Other factors, including year-to-year variations in outflow and 
exports, have also contributed to the decline of the striped bass 
population. California DFG has developed a model suggesting that export 
limitations also are necessary to preserve the striped bass fishery. 
Accordingly, California DFG's recent recommendations to protect striped 
bass have focused on reducing entrainment of fish, eggs and larvae in 
water pumps operated by the SWP and the CVP, rather than on maintaining 
protective salinity conditions (CDFG 1992e, WRINT-DFG-3; D-1630). 
However, according to a series of papers developed for the SFEP-
sponsored workshops, models that are based on the downstream extent of 
low salinity habitat are at least as accurate in predicting striped 
bass abundance as the California DFG model based on flows and exports 
(Jassby, in SFEP 1993b; CDFG 1992e, WRINT-DFG-3). The studies cited 
above suggest that, regardless of the effects of entrainment at the 
diversion pumps, low salinity nursery habitat in Suisun Bay is 
important and that this habitat has sharply declined in recent years. 
Based on these studies, EPA believes that salinity criteria in Suisun 
Bay are necessary to protect nursery habitat of the striped bass.
    --Sacramento splittail. Sacramento splittail (Pogonichthys 
macrolepidotus) are now restricted to the lower reaches of the rivers 
flowing into the Sacramento-San Joaquin Delta and the upper regions of 
the San Francisco Bay complex, particularly Suisun Bay and Suisun Marsh 
(Moyle 1976; Moyle 1980). Historically, this species occurred 
throughout the lowlands of the Sacramento Valley, but diking and 
dredging have eliminated 96% of the wetland habitats this species 
appears to require (Meiorin et al. 1991). Currently, the population 
lives largely in the shallow, low salinity habitat of Suisun Bay and 
Marsh but in early spring adults migrate upstream through the Delta to 
spawn near the mouths of the rivers along the Delta's eastern edge 
(Daniels and Moyle 1983). Although this migration pattern predominates 
for most of the splittail, lower concentrations of the species can be 
found in most locations in the Delta throughout the year.
    In recent years, fewer numbers of newly-spawned splittail have 
moved across the Delta, back to Suisun Bay. Recent severe declines in 
regions in which splittail were formerly abundant resulted in the 
filing of petitions to list the species as endangered under the ESA. 50 
FR 36184 (July 6, 1993). The only other member of the genus, found in 
Clear Lake, California, became extinct in the early 1970's.
    No physiological studies have been done to determine the specific 
salinity tolerances of the splittail, but it is likely that high 
salinities restrict their downstream range. The scarcity of shallow 
habitats upstream and the increase of salinity in Suisun Bay and Suisun 
Marsh have greatly restricted the habitat required by this species.
    Sacramento splittail recruitment displays a strong relationship to 
annual outflow (Daniels and Moyle 1983). The exact mechanism that 
results in this relationship is unclear; years of higher outflow 
provide better cues to direct successful migration upstream by adults, 
larger areas of flooded vegetation on which the adults can spawn 
(Caywood 1974), higher flows to transport the newly spawned young 
downstream, and larger areas of suitable habitat in Suisun Bay and 
Suisun Marsh. Protection of historical habitat conditions in the Bay/
Delta through the implementation of the proposed salinity criteria 
should therefore provide indirect protection for all the needs of this 
species that depend on outflow.
    --Estuary dependent species. In addition to Delta smelt and striped 
bass, several other fish species are dependent on brackish-water 
nursery habitat. The juveniles of these species, collectively referred 
to as ``estuary dependent species'' by the California DFG, live 
predominantly downstream of the Delta within a salinity range of 
approximately 0 to 22 ppt, although the range varies somewhat by 
species. This habitat is larger than the nursery habitat for Delta 
smelt and striped bass, but nevertheless has substantially diminished 
in size as water has been diverted and stored for upstream uses.
    Three of these species, bay shrimp (Crangon franciscorum), starry 
flounder (Platichthys stellatus), and longfin smelt (Spirinchus 
thaleichthys), depend on brackish-water nursery habitat for a 
significant portion of their life cycles. Bay shrimp and starry 
flounder are important components of commercial and sport fisheries, 
and their protection is important to maintain the State's Ocean 
Commercial and Sport Fishing designated uses, as well as the Estuarine 
Habitat designated use.
    The bay shrimp is the largest shrimp species in the estuary, and 
has been the most numerous, except during recent prolonged drought 
conditions, when abundance has been very low. It supports a commercial 
bait fishery in the Bay, and is an important food source for the larger 
fish of the estuary. Reproductive adults and larvae are found in the 
more marine habitats of Central San Francisco Bay and nearshore Gulf of 
the Farallones. Transforming larvae and early juveniles move into the 
Bay from the nearshore ocean, and maturing juveniles are mainly found 
in warm, shallow, brackish water areas (2 to 22 ppt) of the estuary 
(CDFG 1992; WRINT-DFG-6).
    Starry flounder also use the brackish areas of San Francisco Bay as 
nursery habitat. After moving into the Bay as transforming larvae from 
the nearshore ocean during the spring, young-of-the-year juvenile 
flounder (smaller than 70 mm) are found primarily in warm shallows 
where salinities are less than 22 ppt (CDFG 1992, WRINT-DFG-6). By the 
second year of life (1+), the fish have moved out of fresh water 
completely and are concentrated in the brackish water areas of the Bay. 
By the third year of life (2+) they have spread throughout the higher 
salinity areas, and many have migrated out of the Bay.
    Starry flounder supports both a commercial and recreational fishery 
in the San Francisco Bay area. Commercial catch has varied between 486 
thousand pounds in 1980 to a minimum of 40 thousand pounds in 1990. 
Although starry flounder are a small component of the flatfish catch (2 
percent by weight), they are second only to California halibut in price 
per pound at the dock (CDFG 1992, WRINT-DFG-6). Commercial passenger 
fishery total catch and catch per unit effort in San Pablo Bay have 
declined dramatically since the mid-1970's. Abundance of starry 
flounder young-of-the-year and one-year-olds (1+) has been consistently 
low since 1986, and older starry flounder (two years old and older) 
have also declined in the Bay since the mid-1970's, based on Commercial 
Passenger Fishing Vessel logs (CDFG 1992, WRINT-DFG-6).
    Until recently, longfin smelt has been one of the most abundant 
fish species in the estuary. This species spawns in freshwater, and 
larvae and juveniles smaller than 50 mm are predominantly found in 
brackish water with bottom salinities less than 18 ppt. According to 
California DFG, water with less than 18 ppt salinity in the spring 
months of March through June constitutes important nursery habitat for 
longfin smelt (CDFG 1992, WRINT-DFG-6). Recent populations of longfin 
smelt have been very low, and in 1991 the population reached the lowest 
number ever recorded since monitoring was initiated in 1967. As a 
result, this species has been the subject of a petition for listing 
under the ESA. See Petition for Listing Under the Endangered Species 
Act--Longfin smelt and Sacramento splittail, National Heritage 
Institute (November 5, 1992).
    There are close correlations between the location of the near-
bottom 2 ppt isohaline during winter/spring and annual abundance 
indices of bay shrimp, starry flounder, and longfin smelt (Jassby 
1992). Annual abundances are low when the position of the near-bottom 2 
ppt isohaline is upstream and does not move to and remain at a position 
near Roe Island for any extended period of time. Under these 
circumstances, the brackish-water nursery habitat favored by these 
species is primarily limited to Suisun Bay. Salinity data from 
California DFG studies indicate that when near-bottom salinities are at 
or below 2 ppt near Roe Island in Suisun Bay, salinities downstream 
over the large shallow flats of San Pablo Bay are characteristically 
less than 18 to 22 ppt (CDFG 1993). In years when the position of the 
near-bottom 2 ppt isohaline moves downstream at least as far as Roe 
Island in the spring, the area of low-salinity habitat expands into the 
large shallows of San Pablo Bay and these species are more abundant. 
These areas of San Pablo Bay provide greatly increased habitat within 
the salinity ranges preferred by juveniles of these species.
    As with striped bass, other factors are also likely to contribute 
to year-to-year variations in abundance of these species, including the 
strength of net landward bottom currents (shrimp and flounder), coastal 
distribution of reproductive adults and larvae (shrimp and flounder), 
and successful downstream transport and dispersal of larvae and 
juveniles (smelt) (CDFG 1992, WRINT-DFG-6). However, brackish-water 
nursery habitat is essential to the juveniles of these three species, 
and is a major factor in the strong correlation between the position of 
the near-bottom 2 ppt isohaline and abundance. According to studies by 
California DFG, an index of brackish water habitat is strongly 
correlated with abundance indices for these three species (CDFG 1992, 
figs 1-3, WRINT-DFG-6). EPA's proposed salinity criteria, by providing 
estuarine habitat conditions similar to the healthier reference period 
of the late 1960's to early 1970's, should restore and maintain the 
brackish-water nursery habitat required by these three species.
    --Suisun Bay Tidal Wetland Species. The tidal wetlands bordering 
Suisun Bay are characterized as brackish marsh because of their unique 
combination of species typical of both freshwater wetlands and more 
saline wetlands.\7\ Suisun Marsh itself, bordering Suisun Bay on the 
north, is the largest contiguous brackish water marsh in the United 
States. A large portion of the wetland habitat (approximately 44,000 
acres) in this marsh is currently diked and managed for waterfowl use 
and hunting. Approximately 10,000 acres bordering Suisun Bay are still 
fully tidal (Meiorin 1991).
---------------------------------------------------------------------------

    \7\There are currently no salinity criteria protecting the 
Estuarine Habitat, Wildlife Habitat, and other fish and wildlife 
uses of the brackish tidal marshes of Suisun Bay. These large tidal 
marshes are distinct from the ``managed'' marshes in the Suisun Bay. 
EPA's approval of the 1978 Delta Plan criteria was explicitly 
conditioned on the State Board's commitment to develop additional 
criteria for the tidal marshes and to protect aquatic life in the 
Suisun Marsh channels and open waters. Because these conditions have 
not been met, EPA, in its September 3, 1991 letter on the 1991 Bay/
Delta Plan, disapproved the standards for Suisun Marsh and stated 
that the State Board should immediately develop salinity objectives 
sufficient to protect aquatic life and the brackish tidal wetlands 
surrounding Suisun Marsh.
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    These tidal marshes provide habitat for a large, highly diverse, 
and increasingly rare ecological community. The recent ``Status and 
Trends'' reports published by the SFEP listed 154 wildlife species 
associated with the brackish marshes surrounding Suisun Bay (Harvey, et 
al. 1992), including a number of candidates for listing under the ESA. 
These include the Suisun song sparrow (Melospiza melodia maxillaris) 
and the Suisun ornate shrew (Sorex ornatus sinuosus), as well as the 
plants Suisun slough thistle (Cirsium hydrophilum var. hydrophilum), 
Suisun aster (Aster chilensis var. lentus), delta tule pea (Lathyrus 
jepsonii), Mason's lilaeopsis (Lilaeopsis masonii), and soft-haired 
bird's beak (Cordylanthus mollis). These rare species are all found 
exclusively in tidally inundated marsh.
    As part of the SFEP-sponsored workshops, a comprehensive literature 
review and intensive field surveys of marsh vegetation were undertaken 
to document the responses of estuarine marsh communities to changes in 
the salinity regime (Collins and Foin 1993). The study concluded that 
salinity levels in the tidal marshes play a major role in the 
distribution and abundance of plant species. In addition, average tidal 
marsh salinity levels are related to the position of the 2 ppt 
isohaline, although local controls on salinity are important in some 
areas.
    The study also found that recent increases in salinity caused by a 
combination of upstream diversions and drought have adversely affected 
the tidal marsh communities. As salinity has intruded, brackish marsh 
plants which depend on soils low in salt content (especially the tules 
Scirpus californicus and S. acutus) have died back in both the 
shoreline marshes and in some interior marsh channel margins of the 
western half of Suisun Bay. These plants have been replaced by plants 
typically growing in saline soils, especially cordgrass (Spartina 
foliosa). This has been associated with erosion of the marsh margins, 
significantly reducing the tidal marsh acreage in some areas. In 
addition, tules in the upper intertidal zone have been replaced by the 
smaller and more salt tolerant alkali bulrush (Scirpus robustus). These 
changes have significantly affected available habitat for a variety of 
wildlife that nest and feed in these areas, including the Suisun song 
sparrow, marsh wren, common yellowthroat, black-crowned night heron, 
and snowy egret (Collins and Foin 1993; Granholm 1987a; 1987b). The 
loss of habitat for the Suisun song sparrow is of particular concern, 
since individuals of this species are found only in the already 
fragmented marshes bordering Suisun Bay, occupy an established 
territory for their lifetime, and depend on tall tules for successful 
reproduction and cover from predators (Marshall 1948).
    Although there have been no studies of the direct effects of 
salinity on rarer plant species, these species are likely to have the 
same salinity requirements as non-rare species residing in the same 
plant communities. Delta tule pea and Suisun aster are associated with 
tules along the banks of tidal sloughs (CDFG 1991). Mason's lilaeopsis 
is also found along tidal banks, associated with the more freshwater 
marsh species, including tules, and in the shade of riparian shrubs 
such as willows (CDFG 1991). Suisun thistle and soft-haired bird's beak 
are found in the few remaining higher elevation tidal marshes. All of 
these species are limited to marsh areas seasonally inundated with 
fresh to brackish water, and depend on such conditions to varying 
degrees.
    For those brackish marsh plants depending on freshwater conditions, 
the most critical growth period is February through June. If suitable 
lowlands were present upstream, increases in the estuary's salinity 
gradient would allow brackish tidal marsh communities to migrate 
upstream. However, the floodplains and other lowlands suitable for the 
evolution of tidal marshes are absent upstream of Suisun Bay (SFEP 
1993b). As a result, increases in tidal water salinity may 
significantly reduce the already severely limited freshwater and 
brackish marsh habitats, and will threaten the natural diversity of the 
estuary's wetland communities. Maintaining historical levels of low-
salinity habitat in Suisun Marsh is therefore essential to protect 
Estuarine Habitat, Wildlife Habitat, Rare and Endangered Species, and 
other uses designated for protection by the State's water quality 
standards.
d. Proposed Criteria
    (1) Preliminary considerations. This section discusses three issues 
that affect EPA's proposal: the proper level of protection for 
designated uses, the basis for choosing the locations for measuring the 
proposed criteria, and the proper time period for maintaining the 
proposed criteria.
    --Level of Protection. One of the key recommendations of the SFEP-
sponsored workshops was that environmental goals for the estuary would 
be most effective if expressed in terms of restoring conditions to 
those that existed at specific historical periods. If a certain level 
of ecosystem restoration is selected as a goal, then the relationship 
between abundance and the location of the 2 ppt isohaline (and the 
amount of water necessary to achieve that isohaline) can be used as a 
basis for setting standards that will achieve those goals. (SFEP 
1993b).
    This historically-based approach is consistent with EPA's National 
Program Guidance for Biological Criteria for Surface Waters (USEPA 
1990). EPA's National Program Guidance recommends that aquatic 
communities in waterbodies subject to anthropogenic disturbance be 
assessed in comparison to similar, but unimpaired waterbodies (a 
reference condition). Although the Guidance discusses designation of a 
reference site to compare directly with an impaired waterbody, analysis 
of historical records is also recommended. In the case of the Bay/
Delta, a reference waterbody is not available. Instead, reference 
conditions have been based on historical information.
    The proposed salinity criteria reflect estuarine habitat conditions 
that existed prior to 1976. In the recent State Board hearings, EPA, 
NMFS, and USWFS recommended standards that would restore habitat 
conditions to levels that existed in the late 1960's and early 1970's 
(USFWS 1992g, WRINT-FWS-10).\8\ This period generally reflects 
conditions that occurred in the estuary before fish habitat and 
populations began to experience the most recent significant declines, 
and therefore serves as a useful definition of a healthy fishery 
resource. Land use patterns and upstream water developments had largely 
stabilized by the end of this period so that increases in project 
impacts are the dominant change associated with the subsequent decline 
in fishery resources. The reclamation of wetlands was largely complete 
by the 1920's, and the largest of the upstream developments, Shasta 
Reservoir, was completed in the early 1940's.
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    \8\This restoration goal is less protective than the ``without 
project'' goal targeted by the State Board as part of its water 
quality standards in 1978. In the 1978 Delta Plan, the State Board 
adopted standards intended to achieve levels that would have existed 
in the absence of the state and Federal water projects, and agreed 
to revise the standards if necessary to achieve this goal. This 
``without projects'' goal was never formally incorporated into the 
State's water quality standards, and its continued validity as a 
stated goal is in question given the court's decision in United 
States et. al. v. State Water Resources Control Board, supra) 
(reviewing the 1978 Delta Plan and rejecting the ``without 
projects'' approach). EPA continues to believe that fully offsetting 
the impacts of water development should be the goal of long-term 
planning efforts by the State Board and other agencies. However, 
because of the precipitous decline in the biological communities of 
the estuary in the last decade, this goal is no longer reasonably 
attainable in the short term, given the existing physical facilities 
and water project operations in the Delta. As a result, EPA, USFWS 
and NMFS have recommended that the State Board immediately set 
standards sufficient to restore estuarine habitat conditions to 
those that existed in the late 1960's and early 1970's, and to 
establish a long-term goal of fully offsetting the impacts of water 
development (USFWS 1992g, WRINT-FWS-10). This long-term goal is 
consistent with the goals of the recently-enacted Central Valley 
Project Improvement Act (Title 34 of P.L. 102-575, 106 Stat. 4600) 
(Central Valley Project Improvement Act), which include programs to 
mitigate the adverse effects incurred as a result of the 
construction of the CVP.
---------------------------------------------------------------------------

    Ideally, EPA would use the late 1960's to early 1970's habitat 
conditions as both the targeted level of protection and the historical 
reference period. However, to better reflect the natural variability of 
wet and dry years, EPA is proposing criteria that vary according to the 
``water year type''. The water year type concept is already fully 
integrated into the operations of California water management, and the 
State Board's classification of years into one of five categories (wet, 
above normal, below normal, dry, and critically dry) is accepted as the 
standard water year type classification scheme.
    The period of the late 1960's to early 1970's, however, contained 
no dry or critically dry years and only one above normal year. Thus, in 
order to provide an adequate representation of the different water year 
types, EPA is proposing the use of the period 1940 to 1975 as the 
historic reference period. An examination of the historical record 
reveals that this 35 year period was one of fairly consistent 
hydrological conditions. The period is bracketed by major hydrological 
changes--the construction of Shasta Dam immediately before this period, 
and the extended drought and increased water exports beginning 
immediately after this period in 1976.
    Including the longer 1940-1975 period as the historical reference 
period allows better estimation of the salinity regime for different 
water year types than would use of only the late 1960's to early 
1970's. Given that the hydrological conditions were fairly consistent 
throughout the longer 1940-1975 period, EPA believes this longer 
historical reference period serves as a better long term indicator 
through all water year types of the habitat conditions existing in the 
recommended target years of the late 1960's to early 1970's.
    The development of the historical salinity regime is presented in 
appendix II. Salinity records extend back only to 1967, whereas daily 
flow estimates are available from October 1929. Using models created by 
California DWR relating flow and salinity allows reconstruction of the 
salinity regimes in the historical reference period.
    --Basis for locations selected. Three locations for the proposed 2 
ppt isohaline were selected to correspond to protection of three 
different types of estuarine habitat in different water years. 
Together, the use of these three locations will maintain the natural 
variability in salinity levels that characterize the historical data 
set at medium to lower flow levels (those substantially within the 
control of upstream diverters).
    Roe Island. The 2 ppt isohaline occurs at or below Roe Island at 
times of high outflow accompanying storms with uncontrolled runoff, as 
well as at times of high water releases from upstream dams. These flows 
carry many young fish from the Delta downstream into Suisun Bay. 
Because the entrapment zone will consistently be near the broad 
shallows and large marsh areas of Suisun Bay, the young fish and other 
organisms associated with the zone will be distributed into these 
diverse and productive habitats, greatly increasing the extent and 
value of their available habitat. This location will also maximize the 
inputs of production from Suisun Marsh and the shallows of Suisun Bay 
into the entrapment zone, and will provide greatly increased areas of 
medium to low salinity nursery habitat for estuary dependent species in 
San Pablo Bay.
    Chipps Island. The downstream end of Chipps Island marks the 
upstream end of Suisun Bay. As noted above, low salinity habitat in 
Suisun Bay has been well documented as an important nursery area for 
Delta smelt, striped bass, and other estuarine species. Suisun Bay also 
represents the farthest upstream extent of large areas of shallow 
habitat. These shallow habitats are more productive than deeper 
channels (Cloern et al. 1983), and horizontal flows across these 
shallows bring food sources into the entrapment zone. For some species, 
particularly Delta smelt, shallow areas near the entrapment zone are a 
preferred habitat (Moyle et al. 1992), perhaps as a refuge from 
predation. When the average salinity at Chipps Island is less than 2 
ppt, organisms associated with this habitat will be in or near the 
shallow habitats of Suisun Bay for half of each tidal cycle.
    Confluence of Sacramento and San Joaquin Rivers. The confluence of 
the Sacramento and San Joaquin Rivers marks the point where organisms 
associated with low salinity habitat are exposed to the detrimental 
conditions in the lower San Joaquin River. The higher mortalities and 
poorer habitat conditions associated with the lower San Joaquin River 
have been documented at length in testimony to the State Board (USBR 
1992, WRINT-USBR-2; Moyle 1992, WRINT-NHI-9). This location, then, 
provides a suitable upstream limit for the 2 ppt isohaline. When 
average salinities at the confluence reach the 2 ppt level, the 
organisms associated with low salinity habitat will have access to the 
shallow habitats downstream in Suisun Bay only during the lower low 
tide point of the tidal cycle.
    --Period of protection. Changes in water quality that have affected 
aquatic resources have been greatest during the period from February to 
June. Under naturally-occurring hydrological conditions, flows in these 
months were often very large while in summer flow rates declined and 
salinity in the delta increased. Upstream diversions have altered this 
natural pattern by reducing peak spring flows and, in some years, 
increasing flows during the late summer and fall months. The changes in 
summertime water quality (towards lower salinity) occur during a season 
when most of the fish species have already completed their spawning or 
migration (Monroe and Kelly 1992).
    The abundance and reproductive success of almost all species that 
live in or migrate through the upper estuary depend strongly on 
conditions during the months from February through June (Stevens 1977; 
Daniels and Moyle 1983; Stevens and Miller 1983; Moyle and Herbold 
1989; Herbold et al. 1992; SWC 1992, WRINT-SWC-1). These species 
survive and reproduce more successfully when Suisun Bay has large areas 
of low salinity habitat (less than 2 ppt), San Pablo Bay has large 
areas of medium to low salinities (less than 18 to 22 ppt), river 
outflows are high, bottom currents are strong, temperature is low, and 
the areas of greatest turbidity are downstream of the Delta. Because of 
the combination of drought conditions and high levels of water exports, 
these conditions have occurred very rarely in recent years. Therefore, 
EPA's proposed criteria center on these five months.
    (2) Proposed criteria. EPA's specific proposed criteria are shown 
in Table 1. They include 2 ppt salinity criteria at Roe Island, Chipps 
Island, and at the Sacramento/San Joaquin River confluence from 
February through June. The criteria replicate the average number of 
days on which the 2 ppt isohaline occurred at or downstream from each 
of these locations during the historical period 1940-1975, inclusive, 
classified by water year type. Because no critically dry years occurred 
in the period from 1940 to 1975, the required number of days for 
critically dry years is based on an extrapolation of the data.
    The proposed criteria are measured using a 14-day moving average. 
The use of a 14-day moving average allows the mean location to be 
achieved despite the varying strength of tidal currents during the 
lunar cycle because any 14 day period will include the full range of 
spring and neap tidal conditions.

               Table 1.--Proposed 2 ppt Salinity Criteria               
------------------------------------------------------------------------
                                             Roe     Chipps             
                                           Island    Island   Confluence
               Year type                   [km 64]   [km 74]    [km 81] 
                                           (days)    (days)     (days)  
------------------------------------------------------------------------
Wet.....................................       133       148        150 
Above normal............................       105       144        150 
Below normal............................        78       119        150 
Dry.....................................        33       116        150 
Critically dry..........................         0        90        150 
------------------------------------------------------------------------
Numbers indicate required number of days (based on a 14-day moving      
  average) at or downstream from each location for the 5-month period   
  from February through June. The water year classifications are        
  identical to those included in the 1991 Bay/Delta Plan for the        
  Sacramento River Basin. Roe Island salinity shall be measured at the  
  salinity measuring station maintained by the USBR at Port Chicago (km 
  64). Chipps Island salinity shall be measured at the Collinsville     
  station, and salinity at the Confluence shall be measured at the      
  Mallard Slough station, both of which are maintained by the California
  Department of Water Resources. The Roe Island number represents the   
  maximum number of days, based on the adjustment described below.      

    Example: In a wet year, the 2 ppt isohaline must be maintained 
at or downstream of the Confluence at least 150 days during February 
through June, at or downstream of Chipps Island for at least 148 
days during that same period, and, ignoring for a moment the 
adjustment described below, at or downstream of Roe Island for at 
least 133 days.

    Adjusting the Roe Island standard to reflect intra-year storm 
variability. As noted above, the proposed criteria at Roe Island are 
intended, in part, to replicate low salinity habitat conditions 
resulting from spring storm events. Storm events in the spring provide 
many benefits to aquatic resources of the estuary. Large areas of 
flooded vegetation provide ideal spawning for some species, high flows 
transport many planktonic larvae downstream, and translocation of low 
salinity habitat allows wide dispersion of many species which reduces 
predation (and perhaps competition) and replenishes otherwise isolated 
areas. In addition, the variability in salinity over a wide range is 
thought to be an important tool in preventing the buildup of molluscan 
species and, thus, ensures that more food will accumulate in the 
entrapment zone (Nichols 1985; Nichols and Pamatmat 1988).
    The proposed criteria at Roe Island, unadjusted, would fully 
protect low salinity habitat, but would not accurately reflect the 
historical natural variability in runoff and precipitation. The 
distribution of storm systems within the October to April wet season 
varies greatly year-to-year. In some years, all storm events are 
concentrated in early winter, whereas in others the storm events are 
evenly distributed or concentrated in the spring. This natural 
historical variability is reflected in the proposed salinity criteria.
    Without some form of adjustments, salinity criteria at a fixed 
downstream location would also result in more flows through the estuary 
than might be necessary to maintain water quality (that is, the ``water 
costs'' would be unnecessarily high). The flows necessary to hold the 2 
ppt isohaline at a particular location in the estuary are substantially 
less than the flows needed to move that isohaline downstream to a 
different position. In the Bay/Delta, these higher flows used to move 
the isohaline could come either from natural storm events or from 
controlled reservoir releases. The proposed standard provides for an 
adjustment of the Roe Island standard to more closely replicate natural 
spring storm cycles. This adjustment will avoid adverse impacts on 
species (such as the winter-run salmon) dependent on upstream reservoir 
conditions.
    Under the proposal, the criteria of number of days for a given year 
type at Roe Island would not apply unless and until the average daily 
salinity at Roe Island attains the 2 ppt level through natural 
uncontrolled flows. Following the occurrence of such an event, the 14 
day average salinity at Roe Island must not exceed 2 ppt for the number 
of days specified in Table 1. Therefore, the number of days listed 
under Roe Island represents the maximum of the number of days that may 
be required. In effect, this adjustment provides that the additional 
water needed to move the isohaline downstream to Roe Island will come 
from natural storms rather than from reservoir releases or export 
restrictions. This approach better reflects the natural variability in 
timing and quantity of runoff and significantly reduces the water 
supply impacts of the proposed criteria relative to criteria that do 
not account for this variability.
e. Implementation Measures
    Under the CWA, the states have a primary role in developing 
measures implementing water quality criteria. EPA expects that the 
State Board would implement these salinity criteria by making 
appropriate revisions to operational requirements included in water 
rights permits issued by the State Board. Consistent with the mandates 
of section 101(g) of the CWA, the State Board has full discretion in 
determining the source of water flows necessary to meet these criteria. 
EPA has intentionally drafted its proposed criteria to be measured at 
or downstream of the confluence of the Sacramento and San Joaquin 
Rivers. This allows the State Board maximum latitude in choosing a mix 
of flow conditions and export restrictions in both river basins.
    Although the State Board has full discretion to develop an 
implementation plan for these criteria in the manner it chooses, EPA 
and the other federal agencies involved in water resource management 
issues in the Bay/Delta (USFWS, NMFS, and USBR) urge the State Board to 
spread the burden across as broad a spectrum of water users as 
possible. The economic analysis prepared in conjunction with this 
proposal suggests that spreading the burden results in substantially 
lower costs than does imposing the burden on a particular geographical 
area or a narrowly defined group of water users. This is not just a 
matter of fairness. The federal agencies' preliminary discussions with 
water project managers indicated that increasing the pool of 
contributors substantially increases the operational flexibility of the 
water system, and thereby reduces the total impact of meeting the 
proposed criteria. For that reason, the federal agencies hope the State 
Board will continue the concept it adopted in its proposal for D-1630, 
and will allocate the burden of meeting these criteria across the broad 
range of the state's water users.

2. Fish Migration and Cold-Water Habitat Criteria

a. Background
    The State's designated uses for the Bay/Delta include Cold 
Freshwater Habitat to sustain aquatic resources associated with a 
coldwater environment, and Fish Migration to protect those fish which 
migrate through the estuary. The migratory fish species associated with 
the cold-water environment in the Bay/Delta are chinook salmon 
(Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss).
    Currently there are four distinct populations of salmon in the 
Sacramento/San Joaquin river systems, each named for the season of 
their migration upstream as adults. The fall-run population is now the 
most numerous; in recent years, typically 90 percent of all Central 
Valley spawners are fall-run fish. Increased hatchery production of 
fall-run fish has resulted in stable spawning returns of fall-run fish 
passing the Red Bluff Diversion Dam on the Sacramento River; however, 
wild fall-run chinook abundance is low and is decreasing. The 
Sacramento River system still supports small winter-run, spring-run and 
late fall-run populations, but these populations have all declined 
dramatically in recent years (USFWS 1992a, WRINT-USFWS-7). The winter-
run population is now listed as threatened under the ESA. The spring-
run population has recently reached low enough levels to be recognized 
as a species of special concern by the State of California.
    Steelhead trout are also cold-water migratory fish within the 
Sacramento River System. They have suffered a 90 percent decline since 
the late 1960's, and are supported largely by hatchery production (CDFG 
1992a, WRINT-DFG-14).
    The San Joaquin River system supported both fall and spring runs 
until the 1940's when Friant Dam was built. The dam prevented the 
spring-run fish from reaching cool upstream areas suitable for summer 
rearing, so the spring-run disappeared and presently there is only a 
fall-run population. Recently, the San Joaquin population has been 
highly variable, reaching very low levels in times of drought, and 
responding quickly to higher wet year flows. Inadequate stream flows, 
water developments, poor water quality, water diversions, and habitat 
deterioration have had varying degrees of impact. Continuing high 
levels of water diversions from the San Joaquin River and tributaries, 
and high exports out of the South Delta, in concert with the recent 
extended drought have caused major impacts to all San Joaquin tributary 
runs. Population levels are extremely low, and the 1991 brood year may 
only produce a total of 100 to 300 returning adults in 1994 when these 
adults return to spawn at the end of their three year life cycle (CDFG 
1992c, WRINT-DFG-25).
    Salmon and steelhead populations are subject to increased mortality 
when exposed to high temperatures and when diverted out of the main 
channels of the Sacramento and San Joaquin Rivers into less suitable 
habitat. Those fish diverted from the main channels are also subject to 
increased mortality as water exports at the State and Federal pumping 
plants in the south Delta increase. USFWS tagged smolt\9\ studies 
between 1984 and 1989 found that smolts migrating out of the Sacramento 
River system in the spring survived on average approximately 3.4 times 
better in the Sacramento main channel than in the interior (central) 
Delta. Results from studies carried out in the spring of 1985 to 1990 
showed on average approximately 2 times better survival in the main 
channel of the San Joaquin River than in Old River, a secondary 
channel. Higher temperatures affect smolt mortality both in the main 
channel and in the central Delta. For example, the recent (1992) USFWS 
results from spring tagged smolt releases into the central Delta showed 
that mortality was approximately 2\1/2\ times greater at 67  deg.F than 
at temperatures of 63 deg. and 64  deg.F (USFWS 1992a, WRINT-USFWS-7).
---------------------------------------------------------------------------

    \9\A ``smolt'' is a salmon in the process of acclimating to a 
change from a fresh water environment to a salt water environment. 
This occurs when young salmon migrate downstream through the Delta 
to the ocean.
---------------------------------------------------------------------------

    State and federal legislators have recognized the serious threat to 
the continued existence of migratory fishes in the Bay/Delta. In 1988, 
the California State legislature mandated a restoration goal of 
doubling natural salmon and steelhead production by the year 2000, and 
required development of a plan to meet this goal. Salmon, Steelhead 
Trout, and Anadromous Fisheries Program Act; codified at Cal. Fish & 
Game Code Sec. 6900 et seq. (West 1991). In response to this mandate, 
California DFG published the Central Valley Salmon and Steelhead 
Restoration and Enhancement Plan in 1990 (CDFG 1990a). California DFG 
recommended that the State Board adopt an objective of maintaining the 
survival rate of salmon smolts passing through the estuary at the 
``without projects'' historical level, and listed specific actions for 
the consideration of the State Board to implement this objective. Also, 
Congress recently enacted the Central Valley Project Improvement Act, 
which requires that a program be developed and implemented to ensure 
that natural production of anadromous fish in Central Valley rivers and 
streams will be ``sustainable at levels at least twice the average 
levels attained during the period 1967-1991.''
b. Protection of Bay/Delta Coldwater Habitat and Migration Under the 
Clean Water Act
    In order to protect fall-run salmon, the 1978 Delta Plan included 
minimum flow objectives (below those set for striped bass) and mandated 
gate closures to help keep fry out of the central Delta when flows were 
above 12,000 cubic feet per second (cfs) during the period January 1 to 
April 15. In addition, gate closures through May, designed to protect 
striped bass, have also provided protection for out-migrating salmon 
smolts. These measures were considered inadequate by the fisheries 
agencies (USFWS, NMFS, and California DFG). At the 1987 Water Quality 
Control Plan hearings, these agencies recommended flow objectives based 
on 1940 historical flows (without project levels) that would have 
significantly increased protection for fall-run salmon. Similarly, in 
the 1988 Draft Water Quality Control Plan (SWRCB 1988), the State Board 
staff recommended objectives for Sacramento fall-run salmon based on 
average spring flow conditions from 1930 to 1987, and for San Joaquin 
fall-run salmon based on flow conditions from 1953 to 1987. However, 
this Plan was not adopted.
    The 1991 Bay/Delta Plan established additional criteria designed to 
protect salmon. The State Board set new temperature criteria of 68 
deg.F at Freeport and Vernalis from April 1 through June 30 and 
September 1 through November 30 to protect Cold Fresh-Water Habitat for 
fall-run salmon. The 1991 Bay/Delta Plan also set a temperature 
criterion of 66 deg.F at Freeport from January through March to protect 
winter-run salmon. EPA disapproved these criteria because the evidence 
in the State Board's submittal did not demonstrate that they would be 
sufficient to protect cold-water habitat for these species. Based on 
the supporting evidence in the State Board's submittal and the Central 
Valley Salmon and Steelhead Restoration and Enhancement Plan (CDFG 
1990a), EPA recommended that the State Board adopt a 65  deg.F 
criterion, or an alternative that is scientifically defensible. EPA 
also disapproved the State's temperature criteria because they were 
subject to ``controllable factors'' (that is, temperature criteria were 
to be met only if they could be attained using a limited set of 
implementation measures). With this limitation such criteria are 
unlikely to be protective, especially since the State Board 
specifically prohibited the use of reservoir releases to reduce 
temperatures in the Delta (SWRCB, 1991).
    EPA believes that the State should continue to work on developing 
scientifically-defensible long-term temperature criteria sufficient to 
protect cold-water habitat for salmon migrating through the estuary. 
Temperature has been consistently used nationwide as a basis for water 
quality criteria, and there is strong scientific evidence that 
temperature affects survival of salmon smolts as they move through the 
Delta (Kjelson, et al., 1989; USFWS 1992a, WRINT-USFWS-7, USFWS 1992b 
and USFWS 1992c, WRINT-USFWS-8). However, EPA acknowledges that 
specific temperature criteria are difficult to establish and implement 
presently in the Delta because historic temperature levels have been 
highly variable and respond quickly to ambient air temperatures, and 
because there is insufficient information on the effectiveness and 
feasibility of various methods of lowering temperature. It is likely 
that there are short time periods (on the order of days to a few weeks) 
during which efforts at temperature control could be successful and 
provide increased smolt survival. However, existing models predicting 
changes in temperature in response to water project operations use a 
monthly temporal structure and only provide results as monthly means. 
Thus, these models cannot be used to analyze measures that could 
provide improved conditions over shorter periods of time. In addition, 
management of reservoir releases to provide benefits to salmon both in 
the Delta and in the upstream reaches has not been thoroughly assessed 
(Kelley, et al. 1991; Mann and Abbott 1992).
    Studies to develop improved reservoir and river temperature models 
with a shorter time-step and improved predictive capability for the 
entire Sacramento system are just beginning under the auspices of 
Trinity County, the University of California at Davis, and the 
California DFG. These studies will also include a direct analysis of 
the effect of temperature management alternatives on salmon 
populations. Additional work to develop effective temperature models 
has been mandated by section 3406(g) of the recently-enacted Central 
Valley Project Improvement Act. It should be possible to use 
information from these studies to set temperature criteria in the near 
future, and EPA will continue to work with the State to develop 
specific temperature criteria for the Delta. However, at this time, EPA 
is not proposing temperature criteria to replace those criteria 
disapproved in EPA's September 3, 1991 letter, and is instead proposing 
the salmon smolt survival criteria described below.
c. Proposed Smolt Survival Criteria
    Because at this time EPA has not developed an adequate scientific 
basis for precise temperature criteria, EPA is proposing ``smolt 
survival criteria'' to protect the Fish Migration and Cold Fresh-Water 
Habitat designated uses in the Bay/Delta estuary. These criteria are 
based on a smolt survival index that quantifies and predicts the 
survival of salmon migrating through the Delta. The index can be used 
to determine whether the Fish Migration and Cold Fresh-Water Habitat 
uses are impaired in the Bay/Delta. When applied in criteria, the index 
measures and can control the condition of the resource at risk by 
directly assessing and limiting the loss of salmon smolts within the 
Delta due to a variety of impaired water quality conditions. The use of 
this index is consistent with the integrated approach envisioned by the 
National Program Guidance for Biological Criteria for Surface Waters 
(USEPA 1990).
    (1) Smolt Survival Models. The smolt survival indices are based on 
USFWS models described in Kjelson et al. (1989), USFWS (1992a) (WRINT-
USFWS-7) and USFWS (1992b). These models are summarized more fully in 
Appendix III. The models are empirical; that is, they are in large part 
based on the results of experiments measuring and comparing smolt 
survival under a number of different physical conditions of varying 
migration pathways, water temperatures, flow rates, and rates of 
exports from the Delta. The models underlying the salmon smolt survival 
criteria are complex; additional information about the methods used in 
constructing the Sacramento and San Joaquin indices is contained in 
Appendix III and the administrative record to the proposal. For the 
Sacramento River system, the proposed salmon smolt survival criteria 
are based on the most recent model (USFWS 1992b) for predicting 
migration success for the Sacramento River fall-run population, and 
rely on the relationship between smolt survival and three factors: 
temperature, diversion out of the mainstem Sacramento River, and export 
rates. The San Joaquin model is based on experimental data, and relies 
on the relationship between salmon smolt survival and river flows, 
diversion into Old River, and export rates. Consistent with the 
implementation recommendations of USFWS, NMFS, and California DFG, the 
San Joaquin model assumes that a barrier will be in place at the head 
of Old River during the peak migration season.
    Verifying the models used to generate the salmon smolt criteria is 
a continuing process using code-wire tagged smolt studies conducted by 
the USFWS (USFWS 1992b, 1993). Although these models represent the 
present state-of-the-art in Bay/Delta salmon fisheries management, EPA 
anticipates that the models will continue to be verified, updated and 
refined each year by USFWS to reflect additional data collection 
results, and believes that continuing verification is necessary to 
assure that outmigrating smolts are protected. In the event that USFWS 
modifies its models, recommended index values, or recommended 
implementation measures, EPA intends that the criteria will be amended 
accordingly in the next triennial review.
    (2) Proposed Criteria. In developing the goals or target index 
values for its proposal, EPA is relying primarily on the goal of 
restoring habitat conditions to those existing in the late 1960's and 
early 1970's, as recommended in the Interagency Statement of 
Principles. Strict adherence to this recommendation would suggest using 
the index values associated with that historical period as the target 
index values. These values are included in Table 2, which provides 
estimated index values for different historical periods. As part of 
their recent expert testimony to the State Board, USFWS estimated these 
historical survival indices under different conditions (USFWS 1992c, 
WRINT-USFWS-8). The Sacramento River historical values are based on an 
early version of the Sacramento River model (Kjelson et al. 1989). 
There would be minor changes in the estimates using the most up-to-date 
model (USFWS 1992b). For example, recalculating the Sacramento River 
value for the 1956-1970 historical period yields a mean of the five-
year types of .37, compared to the .36 indicated in Table 2.

  Table 2.--Historical Salmon Smolt Survival Indices for the Sacramento 
              and San Joaquin River Portions of the Delta               
------------------------------------------------------------------------
                                  WATER YEAR TYPE                Mean of
                   ---------------------------------------------   year 
                       W        AN       BN       D        C      types 
------------------------------------------------------------------------
Sacramento River                                                        
 goal:                                                                  
    1940 Level of                                                       
     Development..      .76      .81      .77      .63      .44      .68
    1956-70                                                             
     Historical...      .56     a.45      .35      .26     a.20      .36
    1960-88                                                             
     Historical...      .44      .43      .31      .25      .19      .32
    1978-90                                                             
     Historical...      .39     a.32     a.28      .22      .16      .27
San Joaquin River                                                       
 Goal:                                                                  
    1940 Level of                                                       
     Development..      .58      .50      .52      .47      .39      .49
    1956-70                                                             
     Historical...      .61     a.25      .18      .17     a.15      .27
    1960-88                                                             
     Historical...      .43      .12      .17      .13      .12      .19
    1978-90                                                             
     Historical...      .48     a.15     a.09     *.06      .07    .17* 
------------------------------------------------------------------------
aInterpolated: there were no water years in these categories during the 
  relevant historical period. Source: USFWS 1992a.                      

    For a number of reasons, however, strict adherence to the late 
1960's and early 1970's target is inappropriate. Salmon fisheries, 
especially on the San Joaquin River, were already somewhat degraded 
during that historical period, and the degradation has been more severe 
in drier years. This is demonstrated in Table 2, above, which provides 
estimated historical survival index values for the relevant period. 
This Table shows that the decline in the survival index was more 
pronounced in critical, dry, and below normal water years than in 
wetter years. Accordingly, to protect salmon from falling to 
dangerously low population levels, and more nearly mimic the natural 
historical response of smolts migrating through the Delta to year-to-
year changes in hydrology, EPA is proposing more protective target 
values in drier years and less in wetter years.
    On the Sacramento River system, EPA believes salmon smolt migration 
will be protected if the long-term average survival over all water year 
types replicates the target historical period values. Protection at the 
late 1960's to early 1970's level in the wetter years is not necessary 
if better protection is afforded migrating smolts in the drier years. 
On the San Joaquin River system, however, the drop in survival has been 
more severe in drier years, the runs are smaller and more at risk, and 
the overall survival index was less than in the Sacramento system 
during the target historical period. For that reason, in order to 
protect the Fish Migration designated use on the San Joaquin, EPA is 
proposing index values that afford both better protection in drier 
years and overall index values that are higher than in the historical 
late 1960's to early 1970's period.
    To achieve this level of protection and to address this bias in the 
historical reference period index values, EPA is proposing the use of 
target values derived from the recommendations and analyses carried out 
by the Delta Team of the Five Agency Chinook Salmon Committee. This 
interagency group consists of representatives from the USFWS, 
California DFG, California DWR, NMFS, and USBR. Its reports (Five 
Agency Delta Salmon Team, 1991a, 1991b) represent a consensus on the 
most effective and feasible implementation measures to protect 
downstream migrant salmon smolts in the Delta. In preparing its 
recommendations for the 1992 State Board hearings, USFWS reviewed 
recommendations from the Five Agency Delta Salmon Team in its salmon 
smolt model, and presented a set of index values and corresponding 
operational recommendations to the State Board (USFWS 1992a, WRINT-
USFWS-7; USFWS 1992c). These index values, which are intended to be 
consistent with the fisheries agencies recommended target index values 
that would restore habitat conditions and salmon populations to those 
characteristic of the late 1960's to early 1970's (USFWS 1992a, WRINT-
USFWS-7; USFWS 1992c, WRINT-USFWS-8; CDFG 1992b, WRINT-DFG-8), are 
shown in Table 3. The values for the Sacramento River index differ 
slightly from those presented in the 1992 State Board hearings because 
these Table 3 values are based on the most recent version of the 
Sacramento River model.

  Table 3.--Salmon Smolt Survival Indices Based on Five Agency Chinook  
              Salmon Committee Analysis and Recommendations             
------------------------------------------------------------------------
          Sacramento River                    San Joaquin River         
------------------------------------------------------------------------
                              Index                                Index
      Water year type         value        Water year type         value
------------------------------------------------------------------------
Wet........................     .49  Wet........................     .46
Above Normal...............     .41  Above normal...............     .30
Below Normal...............     .40  Below normal...............     .26
Dry........................     .35  Dry........................     .23
Critical...................     .32  Critical...................     .20
Mean.......................     .41  Mean.......................     .31
------------------------------------------------------------------------

    Finally, in arriving at index values for its proposal contained in 
Table 4, EPA has adjusted the index values of Table 3 to meet concerns 
over potential closure of the Georgiana Slough. As discussed below, EPA 
has been engaged in consultations with USFWS and NMFS under the ESA 
about possible effects of EPA's water quality standards actions on 
threatened and endangered species. During the course of these 
consultations, it was suggested that one of the measures the Five 
Agency Chinook Salmon Committee had recommended as an effective 
protective measure for salmon smolts--putting a temporary barrier at 
the head of Georgiana Slough--may have deleterious effects on the Delta 
smelt and other native aquatic life in the central Delta, and possibly 
on adult salmon returning upstream. For that reason, EPA has recomputed 
the index values (see Table 4) to reflect model results if the 
Georgiana Slough were left open. Lower exports, particularly during 
times of peak San Joaquin salmon outmigration, were incorporated as an 
additional feasible and effective implementation measure benefiting 
salmon, in part to compensate for the additional mortality associated 
with keeping Georgiana Slough open. EPA believes that these adjustments 
still provide protection consistent with the goal of restoring habitat 
conditions to those existing in the late 1960's to early 1970's (mean 
Sacramento River survival index of .37), while also taking into account 
achievable implementation measures. The recomputed index values in 
Table 4 are included as EPA's proposal.

                Table 4.--Proposed Salmon Smolt Criteria                
------------------------------------------------------------------------
          Sacramento River                    San Joaquin River         
------------------------------------------------------------------------
                              Index                                Index
      Water year type         value        Water year type         value
------------------------------------------------------------------------
Wet........................     .45  Wet........................     .46
Above Normal...............     .38  Above normal...............     .30
Below Normal...............     .36  Below normal...............     .26
Dry........................     .32  Dry........................     .23
Critical...................     .29  Critical...................     .20
------------------------------------------------------------------------

    To protect both Fish Migration and Cold Fresh-Water Habitat 
designated, EPA proposes that the specific smolt survival criteria in 
Table 4, above, be adopted for the Bay/Delta. As explained above, the 
proposed Sacramento River criteria are modified from the USFWS indices 
in Table 3. The San Joaquin River criteria are the same as Table 3. The 
Sacramento River criteria provide overall protection at approximately 
the 1956-1970 historical level (.37 mean survival index). The San 
Joaquin River criteria provides better protection than the 1956-1970 
historical level (.27 mean survival index). Both sets of criteria 
provide better protection than the 1956-1970 historical period in drier 
years, and less protection in wetter years. These criteria should 
provide more consistent smolt survival and help avoid situations where 
extraordinary measures are necessary to preserve runs, particularly in 
the San Joaquin River tributaries. Water year type designations are 
identical to State Board classifications (SWRCB 1992a).
d. Implementation Measures
    Under the CWA, the States have a primary role in developing 
measures implementing water quality criteria. EPA expects that the 
State Board would implement these criteria by making appropriate 
revisions to operational requirements included in water rights permits 
issued by the State Board. EPA believes that the State Board would have 
a number of possible implementation approaches for achieving the salmon 
smolt survival criteria. In the recent State Board hearings, USFWS 
recommended a series of implementation measures (based on the Five 
Agency Chinook Salmon Committee proposals) designed to achieve the 
smolt survival indices recommended in the joint statement by USFWS, 
NMFS and EPA. For the Sacramento River, these included closure of the 
Delta Cross Channel from April through June, closure of Georgiana 
Slough from April 15 to June 15, and minimum Sacramento Flow at Rio 
Vista of 4000 cfs from April through June. For the San Joaquin River, 
these measures included requiring a range of flows from 2,000 to 10,000 
cfs at Vernalis from April 15 to May 15; requiring minimum flows of 
1000 cfs at Jersey Point from April through June, except from April 15 
to May 15, when higher flows from 1000 to 3000 cfs would be required; 
and placing a full barrier in upper Old River from April through May. 
Total water exports would be curtailed to a range from 6000 cfs in wet 
years to 2000 cfs in critically dry years from April 15 to May 15.
    Based on the USFWS models, these particular measures will achieve 
the proposed smolt survival indices in Table 3. However, as discussed 
earlier, EPA has incorporated into its proposed target index values 
changes to the recommended implementation measures based on concerns 
about the effect of these measures on other aquatic resources. Given 
the nature of the index itself, however, there is substantial 
flexibility in how the target values can be achieved. For example, if 
flows are increased above the recommended levels in the San Joaquin 
River, the associated export limits could also be increased while 
achieving the same level of protection. Reductions in Sacramento River 
temperatures would also provide significant benefits. Although 
temperature controls were not included in the USFWS recommendations, 
they are an important variable in the USFWS model, and may be the most 
significant factor affecting smolt survival in the Sacramento River 
system. Implementation measures affecting temperature may therefore be 
an effective means of attaining the smolt survival criteria.
    There is also evidence that short-term operational changes 
implemented at peak migration times coincident with critical periods of 
high ambient air and water temperature may provide significant benefits 
(Kelley, et al, 1991). Other possibilities listed in California DFG's 
Central Valley Salmon and Steelhead Restoration and Enhancement Plan 
(CDFG 1990) include screening Georgiana Slough and screening the Delta 
Cross Channel. A sound barrier (a device generating subsurface sound 
that discourages fish from entering the Slough) at Georgiana Slough is 
currently under study and may also be a useful implementation measure. 
As new methods are developed to increase smolt survival, their benefits 
can be assessed, and their contribution toward meeting and/or revising 
the criteria taken into account.
    Given this potential flexibility, EPA believes that establishing 
smolt survival indices as Fish Migration and Cold Fresh-Water Habitat 
criteria would give the State Board maximum latitude in choosing a set 
of implementation methods that will attain protection of the designated 
migration and coldwater fisheries uses. As such, these proposed 
criteria are consistent with the mandates of section 101(g) of the CWA, 
as discussed above, and accommodate the State's interest in allocating 
its water supplies in a way that maximizes the many values important to 
the State. Furthermore, the proposal of these criteria is consistent 
with the authority in CWA section 303(c)(4), which authorizes EPA to 
propose revised or new standards to meet the requirements of the Act.
e. Protection of Other Salmon Runs and Life Stages
    Because the smolt survival indices were developed using tagged 
fall-run fish during the time of their outmigration, EPA is proposing 
the use of these indices only for fall-run outmigrants. For winter-, 
late fall-, and spring-run salmon, as well as steelhead, there is no 
direct information about the factors that affect survival, although it 
is likely that many of the same factors, with the exception of 
temperatures during the colder months, are also affecting the juveniles 
of these populations as they migrate through the Delta.
    Measures implemented by the USBR and SWP as a result of the 
Biological Opinion for winter-run salmon issued by NMFS under the ESA 
afford some protection for other runs, in addition to protection for 
the winter-run salmon population itself. NMFS, Biological Opinion on 
Central Valley Project, 1992 Operations (February 14, 1992). In 
addition, EPA has been consulting with NMFS to assure that the 
implementation of EPA's proposed standards will not jeopardize the 
winter-run Chinook salmon population.
    Juvenile spring-run salmon and steelhead move through the Delta 
during the same period as winter-run and fall-run salmon, and should be 
protected in the Delta by measures taken for these other runs. Late 
fall-run salmon, however, outmigrate in fall and early winter, and are 
currently not fully protected during their passage through the Delta. 
Protective criteria for this run should be developed by the State Board 
in the near future to ensure that this run is protected.
    Younger salmon, or fry, also enter the Delta, particularly when 
rainstorms stimulate the movement of fry out of the tributaries and 
into the lower Rivers and Delta. Some protection for these fry is 
afforded by the current State Board standards requiring closure of the 
Delta Cross Channel gates when flows are higher than 12,000 cfs. 
However, closure of the Cross Channel gates alone may not be protective 
enough, since fry can be swept into the central Delta through Georgiana 
Slough and upstream to the export pumps when there is reverse flow in 
the lower San Joaquin River, especially during times of high export. 
For that reason, Delta habitat conditions for fry may need to be 
addressed by the State Board in the future.
f. Protection of Other Migrating Species
    Species other than salmonids seasonally migrate into and out of the 
Delta for spawning and as juveniles. These species include striped 
bass, Delta smelt, longfin smelt, white and green sturgeon, American 
shad and Sacramento splittail. With the exception of temperature, the 
factors that lead to successful migration of salmonid smolts are also 
important for successful migration of the juveniles of these species 
into the lower embayments. Therefore, EPA's proposed salmon smolt 
survival criteria, although specifically addressing fall-run Chinook 
salmon, will also help protect migration of these other migrating 
species.

3. Fish Spawning Criteria

a. Background
    In California, striped bass spawn primarily in the warmer 
freshwater segments of the Sacramento and San Joaquin Rivers. 
Protection of spawning in both river systems is important to ensure the 
genetic diversity of the population as well as to increase the size of 
the overall striped bass population. Adults spawn by migrating upstream 
from the San Francisco Bay or from the Pacific Ocean (Stevens 1979; 
Wang 1986). The precise location and time of spawning appear to be 
controlled by temperature and salinity (Turner 1972a; Turner and 
Chadwick 1972). According to the California DFG, striped bass spawn 
successfully only in freshwater with electrical conductivities less 
than 0.44 millimhos10 per centimeter electroconductivity (mmhos/cm 
EC), and prefer to spawn in waters with conductivities below 0.33 
mmhos/cm. Conductivities greater than 0.55 mmhos/cm appear to block the 
upstream migration of adult spawners (Radtke and Turner 1967; SWRCB 
1987; CDFG 1990b, WQCP-DFG-4).
---------------------------------------------------------------------------

    \1\0The salinity problems addressed by the isohaline criteria 
outlined above are caused primarily by salt water intrusion and are 
traditionally measured by ``parts per thousand''. In contrast, 
salinity conditions upstream in freshwater are generally affected by 
dissolved salts from upstream water runoff. The salinity content of 
freshwater is traditionally measured by its electroconductivity or 
``EC'' standardized to 25 C (specific conductance), and is expressed 
in terms of millimhos per centimeter electroconductivity or ``mmhos/
cm EC''.
---------------------------------------------------------------------------

    In the Sacramento River, adults migrate to spawning sites upstream 
of Sacramento until they encounter the appropriate warmer temperatures 
for spawning. Because of the higher volume of water in the Sacramento 
River and the particular constituents and volume of nonpoint source 
discharges into the river, salinity does not appear to be a serious 
limitation on spawning at any location along the river. In years of 
higher spring river flows, with correspondingly lower water 
temperatures, bass can spawn further upstream and later in the April-
June period because the warmer temperatures that induce spawning occur 
later (Chadwick 1958). Migration and spawning in the Sacramento River 
are therefore not adversely affected by salinity. In the smaller and 
shallower San Joaquin River, however, the earlier occurrence of warm 
temperatures causes the peak spawning period to occur earlier than in 
the Sacramento River; the San Joaquin peak usually occurs in April or 
May rather than in May or June (Chadwick 1958). Migrating bass seeking 
the warmer waters encounter excessive upstream salinity caused 
primarily by runoff. This salinity can block migration up the San 
Joaquin River, thereby reducing spawning, and can also reduce survival 
of eggs (Farley 1966; Radtke 1966; Radtke and Turner 1967; Turner and 
Farley 1971; Turner 1972a, 1972b).
    The State Board's 1991 Bay/Delta Plan established objectives of 1.5 
mmhos/cm EC at Antioch and 0.44 mmhos/cm EC at Prisoners Point in April 
and May. EPA disapproved these objectives, in part, because they are 
not adequate to protect spawning habitat in the reach farther upstream 
between Prisoners Point and Vernalis.
    In the 1987 State Board hearings, California DFG testified that 
striped bass formerly spawned farther up the San Joaquin River, but 
that this has occurred less frequently in recent years because of 
increased salinity levels (CDFG 1987). Salinity in the San Joaquin 
River increases upstream of Prisoners Point due to reduced freshwater 
inflow and agricultural return flows. Thus the absence of salinity 
criteria above Prisoners Point effectively establishes a barrier to 
adult migration and spawning farther upstream on the San Joaquin River 
(Turner 1972a,b). California DFG also suggested that there was a danger 
of losing the part of the population that spawned in this area if high 
salinities prevent spawning or decrease survival of newly spawned eggs 
(CDFG 1987; SWRCB. Phase I Hearing Transcript, LXXV, VII 111:3-14).
    In the 1991 Bay/Delta Plan, the State Board described several 
alternative water quality standards that would have extended the 
protection of spawning conditions upstream of Prisoners Point, 
including one alternative very similar to the one EPA is proposing 
today. However, the State Board deferred adoption of revised standards, 
apparently because of concern that improved spawning conditions would 
lead to greater losses of young to entrainment at the State and Federal 
pumping plants. As indicated in its September 3, 1991 letter 
disapproving certain State criteria, EPA believes that the State Board 
can, in developing its implementation measures, address the impact of 
the pumps on this spawning habitat.
    EPA also disapproved the 1991 Bay/Delta Plan spawning criteria 
because they were not based on sound science. The State Board explained 
that the 1.5 mmhos/cm EC criteria at Antioch was intended to protect 
spawning habitat upstream of Antioch (near Jersey Point), not at the 
Antioch location itself. The State Board acknowledged that ``the use of 
1.5 [mmhos/cm] EC at Antioch appears not to be generally appropriate, 
and proposed that a thorough review of this [criteria] be undertaken at 
the next triennial review'' (1991 Bay/Delta Plan, p. 5-32). EPA found 
this indirect and unproven approach of setting criteria downstream in 
hopes of attaining different criteria upstream deficient, and 
disapproved it. EPA's proposed criteria would correct this deficiency 
by establishing the scientifically-defensible criteria at Jersey Point, 
the actual point of concern.
    The State Board also acknowledged that the 1991 Bay/Delta Plan 
spawning criteria did not protect the spawning reach in the lower San 
Joaquin River, but instead only at two locations: Jersey Point and 
Prisoners Point (1991 Bay/Delta Plan, p. 5-30). As a result, the State 
Board directed California DFG to study how a specific habitat zone of 
0.44 mmhos/cm EC could be established in the entire reach between 
Jersey Point and Prisoners Point ``to make certain that the State Board 
develops water quality objectives that are based on sound scientific 
data'' (1991 Bay/Delta Plan, p. 5-33). EPA agrees, and is proposing 
criteria to assure that the entire reach between Jersey Point and 
Prisoners Point should be protected.
b. Proposed Criteria
    In its September 3, 1991 letter and subsequent correspondence with 
the Board, EPA recommended salinity criteria of 0.44 mmhos/cm EC in the 
lower San Joaquin River in the reach from Jersey Point and Vernalis. 
After further reviewing the scientific evidence, EPA is proposing the 
following criteria:

    The 14-day running average of the mean daily EC shall not be 
more than 0.44 mmhos/cm for the period April 1 to May 31 in wet, 
above normal, and below normal years at the following stations: 
Jersey Point, San Andreas Landing, Prisoners Point, Buckley Cove, 
Rough and Ready Island, Brandt Bridge, Mossdale, and Vernalis. In 
dry and critical water years, the criteria are required only in the 
reach between Jersey Point and Prisoners Point, as measured at 
Jersey Point, San Andreas Landing, and Prisoners Point.

    These criteria will fully protect the historic spawning range of 
striped bass on the lower San Joaquin River, while reflecting the 
natural variability in salinity levels in different water year types.
c. Implementation
    Under the CWA, the states have a primary role in developing 
measures implementing water quality criteria. EPA expects that the 
State Board would implement these criteria by making appropriate 
revisions to operational requirements included in water rights permits 
issued by the State Board.

4. Compliance With Endangered Species Act

    EPA has concluded that its promulgation of water quality criteria 
for the Bay/Delta may affect certain species protected by the federal 
ESA. These include the winter-run chinook salmon (listed as threatened 
and proposed for reclassification as endangered), the Delta smelt 
(listed as threatened), and the Sacramento splittail and longfin smelt 
(both the subject of petitions for listing). There are also a number of 
listed and proposed species resident in Suisun Marsh. Under section 7 
of the ESA and accompanying regulations, EPA is required to consult 
with NMFS (on the winter-run chinook salmon) and USFWS (on the other 
listed and proposed species) to assure that the water quality criteria 
promulgated by EPA do not jeopardize the continued existence of these 
species or adversely affect their critical habitat. 50 CFR 402.14 and 
Sec. 402.10.
    EPA has worked closely with NMFS and USFWS over the past two years 
to meet its obligations under the ESA. The federal agencies have 
recognized the need to take an integrated ecosystem approach to the 
Bay/Delta rather than a fragmented, species-by-species approach. To 
that end, the EPA, NMFS, and USFWS issued a joint proposal to the State 
Board's 1992 hearings on interim measures recommending that the State 
Board adopt an immediate goal of restoration of habitat conditions to 
those characteristic of the late 1960's and early 1970's. By targeting 
this level of protection, the agencies intended to establish habitat 
conditions that would protect and preserve the entire range of fish and 
wildlife uses in the Bay/Delta.
    The criteria proposed in this notice follow this approach to 
habitat protection within the Bay/Delta watershed. Pursuant to 50 CFR 
Secs. 402.14, EPA has initiated formal consultations with USFWS and 
NMFS on the potential effects of its action on endangered and 
threatened species. The agencies have agreed to finalize these 
consultations before EPA promulgates water quality standards in the 
Bay/Delta.
BILLING CODE 6560-50-P

TP06JA94.005


TP06JA94.006


TP06JA94.007


BILLING CODE 6560-50-C

D. Executive Order 12866

    Executive Order 12866 requires EPA and other agencies to assess the 
potential costs and benefits of all significant regulatory actions. 
Significant regulatory actions are those that impose a cost on the 
economy of $100 million or more annually or have certain regulatory, 
policy, or economic impacts. Today's proposed rule meets the criteria 
of a significant regulatory action set forth in section 3(f) of the 
Executive Order. The regulatory analysis for this proposed rule is 
presented in ``Draft Regulatory Impact Assessment of the Proposed Water 
Quality Standards for the San Francisco Bay/Sacramento-San Joaquin 
River Delta'' (see Section F for the availability of this and other 
documents). This draft RIA was submitted to OMB for review as required 
by the Executive Order.
    EPA's action is the proposal of water quality standards and this 
action explicitly does not include a proposed implementation plan. The 
implementation plan has not yet been developed by the State. Therefore, 
this draft RIA analyses a range of possible implementation scenarios. 
Importantly, the analysis illustrates that the level of costs for the 
same level of environmental benefits varies significantly depending on 
assumptions in implementation scenarios. Specifically, mechanisms for 
economically-efficient allocation of water or for the widespread 
distribution of responsibility, such as water transfers and/or a 
drought water bank, result in the most cost-effective scenarios.
    EPA is committed to working with the State on an implementation 
plan and welcomes additional information and analysis on the economic 
costs and benefits of its proposals. EPA is interested in both improved 
information and policies and programs to minimize the economic impacts 
upon water users.
    The draft RIA evaluated the costs and benefits of the combined 
federal proposals, including EPA's proposed water quality standards and 
USFWS's actions under the ESA. The primary method of implementation is 
assumed to be increased Delta outflow resulting in reduced water 
supplies to urban and agricultural water users. Further, critical 
habitat designation may result in additional costs by possibly limiting 
sand and gravel operations and affecting marina operations. Benefits 
are to the Delta ecosystem as a whole, species diversity, and 
commercial and recreational fisheries.

Assessment of Costs and Impacts

    The draft RIA shows that the costs to both agricultural and urban 
water users would depend upon how water supplies are allocated to 
implement the proposals.
     The primary method for implementing the combined federal 
proposals will be increases in Delta outflow. Current estimates of the 
additional outflow developed by the California DWR are 540,000 acre-
feet on average and 1.1 million acre-feet in critically dry years.
     The analysis uses an initial distribution of water supply 
reductions between agricultural users (80% of the reductions) and urban 
users (the remaining 20%).
    The results of three scenarios analyzed are presented in the draft 
RIA and are briefly summarized here.
     Agricultural impacts are influenced by improved irrigation 
efficiency, crop shifting opportunities, the size of the affected 
region and opportunities for water trading between agricultural 
districts. A range of these options was modeled, except for irrigation 
efficiency.
     A middle range distribution of supply impacts (Scenario 2) 
that includes water trading between agricultural districts results in 
producer surplus losses (net revenue losses) of $20 million dollars on 
average. If trading is limited (Scenario 1), impacts are estimated to 
be $44 million on average. Scenario 3 illustrates the lowest cost 
option, distributing the water supply reductions throughout the Central 
Valley, resulting in producer surplus losses estimates of $8 million on 
average.
     Economic impacts were estimated for critically dry years 
and indicate larger economic impacts, because lower cost options are 
already used up in drought years. Scenario 1, where trading is limited, 
estimates $147 million in costs in critically dry years. Scenario 2, 
where trading is facilitated among agricultural districts, reduces 
those impacts by nearly half to $87 million in impacts.
    Potential impacts on the urban users were more difficult to 
estimate, given the less-established analytic information base. Three 
scenarios were developed to project the economic impacts based upon 
different assumptions and implementation choices. Key implementation 
choices analyzed include the availability of transfers, drought water 
pricing, a drought water bank and increased water reclamation. 
Additional water management choices include increased conservation, 
conjunctive use and other demand management programs.
     Water transfers and an efficient drought water bank are 
key to minimizing impacts on urban users, given increased environmental 
needs. In the least-cost scenario, (Scenario 3) impacts on urban users 
were projected to be $25 million on average.
     Under Scenario 2, where reclamation meets urban supply 
needs along with a combination of drought water pricing and a more 
limited drought water bank, impacts are approximately $50-54 million on 
average. Under Scenario 1, where no drought water bank exists, impacts 
are projected at $80 million on average.
     The economic impacts of the proposals are highest in 
drought years, when fewer supplies are available to meet increased 
urban and environmental needs. Estimation of consumer surplus losses 
for Scenario 3 projects a continuation of the 1991 drought water bank 
resulting in economic costs of $70 million in a critically dry year. A 
combination of a more limited drought water bank and drought water 
pricing results in consumer surplus losses of $184-223 million for 
Scenario 2. Scenario 1, where no drought water bank exists, results in 
consumer surplus losses of $450 million in a critically dry year. 
However, EPA projects that these losses are not likely given the 
support for a drought water bank as a drought management option. 
Further, consumer surplus losses do not measure water bill increases in 
the drought case because consumers have demonstrated in drought periods 
that they change their water use practices rather than pay higher 
rates. Accordingly, an undetermined portion of these estimates is the 
value of inconvenience and changes in behavior during drought.
    In addition, the draft RIA also estimated employment impacts for 
agriculture associated with the implementation of these proposals. The 
direct employment effects were estimated to be a reduction of 99 
person-years on average, but 1926 person-years in a critically dry year 
for Scenario 2 (water trading allowed between agricultural districts). 
If water trading between agricultural districts is limited, employment 
impacts are estimated to be higher, with 828 person years on average 
and 3282 person years in a critically dry year. These estimates are not 
predicted employment changes (e.g impacts that would effect the actual 
unemployment rate) because they do not account for a full labor market 
equilibrium analysis.

Assessment of Benefits

    Background: The Bay/Delta estuary constitutes one of the largest 
habitats for fish and wildlife in the United States. The estuary 
supports more than 120 fish species and provides a stopover or home for 
more than half of the waterfowl and shorebirds migrating on the Pacific 
Flyway. Suisun Marsh, which is within the Bay/Delta estuary, supports 
many rare plant and animal species. Maintenance of freshwater, 
estuarine, and wildlife habitat would preserve rare and endangered 
species; permit fish migration; and provide opportunities for 
commercial ocean fishing and sport fishing.
    Qualitative assessment: The combined proposed requirements will 
increase the protection of the estuarine habitat in the Delta and will 
benefit the ecosystem overall. In addition, the combined proposal is 
expected to increase biological productivity of such important 
resources as salmon, striped bass, and waterfowl; protect diversity of 
species, such as Delta smelt, longfin smelt and Sacramento splittail, 
that are unique to the Bay/Delta ecosystem; increase commercial and 
recreational fishing opportunities; and increase opportunities for 
wildlife observation resulting from restoration of riparian and tidal 
marsh habitat and ecosystem.
    Benefits associated with the federal proposals are described 
qualitatively for most ecosystem benefits. Some fish population 
increases were estimated and a portion of the commercial and 
recreational fishery benefits were monetized.
     The benefits of the federal proposals are an increase in 
biological productivity and ecosystem health for the Bay/Delta 
ecosystem. This increase includes protecting unique species from 
extinction. Bay/Delta species that currently might qualify for listing 
under the ESA include the longfin smelt, spring-run Chinook salmon, 
Sacramento splittail, green sturgeon, and Red Hills Roach, in addition 
to the already listed winter-run Chinook salmon and Delta smelt. A 
potential benefit of the federal proposals is that the ecosystem health 
might improve to the point where unlisted species need not be listed, 
or presently listed species could be delisted under the ESA.
     Well-established relationships between estuarine 
conditions and populations exist for many estuarine species. The extent 
of the low salinity habitat in the estuary is closely associated with 
the abundance and distribution of estuarine species at all trophic 
levels. Increased populations were estimated for salmon (increasing by 
approximately 90,000 salmon), striped bass (increasing by approximately 
10 percent), and starry flounder. In addition, populations of other 
game species of green and white sturgeon, bay shrimp, American shad and 
white catfish are expected to increase.
     A portion of these population increases will accrue to the 
recreational or commercial fisheries. Not less than $9-11 million 
annually were estimated, again with many benefits not estimated in 
dollar value. The majority of these gains are in the commercial salmon 
fishery. Employment gains in the salmon fishery were estimated to 
increase by 300-360 jobs annually.
     Many other recreation activities, including hunting, 
boating, and nature appreciation are expected to be enhanced by the 
proposed regulations; however, the estimated change in participation in 
these activities could not be quantified.
     Enhancing the natural environment of the Bay/Delta would 
have nonuse social benefits. Although these benefits could not be 
quantified, it is believed that they constitute the largest portion of 
the total value to society of implementing the proposed regulations.
     Enhancing water quality in the Bay/Delta could result in 
other benefits associated with the avoidance of listing additional 
species and associated increased flexibility in water management and 
the avoided costs of further collapse of the ecosystem and its 
associated fisheries and dependent communities.

Summary of Costs and Benefits

    Monetized social costs and benefits of the federal proposals are 
not directly comparable in this analysis because some use benefits to 
fisheries and non-use benefits of ecological improvement and species 
diversity cannot be estimated. However, two conclusions can be drawn:
     The implementation plan for the federal proposals has not 
yet been developed, thereby making it difficult to project actual 
levels of economic impacts. However, it is reasonable to assume that 
cost-effective solutions will be pursued that include a flexible 
approach to meeting Delta requirements. Thus, economic costs in the 
agricultural sector are estimated to be $20 million on average and $25 
million for the urban sector. However, the overall costs may be lower 
than the total, given that at least some of the increases in urban 
costs will be payments to agriculture for water transferred. The 
benefits are estimated to be $10 million from improved commercial 
fisheries, and unquantified but important ecological, scientific, 
educational and existence values.
     Costs and benefits are difficult to compare directly in 
this case because of the non-marginal nature of ecosystem protection 
and species protection. These benefits, including preventing the 
extinction of several candidate or listed species and preventing the 
collapse of the Bay/Delta ecosystem, account for the majority of 
benefits.
     Given both the monetary estimates of benefits and the 
qualitative information on benefits not expressed in dollar value, EPA 
believes that the proposal can be implemented in a cost-effective 
manner where a healthy estuary and fisheries can co-exist with a strong 
agricultural and urban sector. Given all the available information, the 
benefits are commensurate with the costs.
     Comprehensive analyses of the incremental response of 
costs and benefits to marginal changes in EPA's proposed rule have not 
been prepared. However, EPA has developed in the draft RIA a method for 
roughly estimating incremental changes in economic costs based on 
changes in the number of days of compliance with the proposed salinity 
criteria at particular locations in the estuary. These estimates are 
based on the estimates of the flows necessary to maintain the criteria 
at the target locations. For example, the difference in water supply 
impacts between a day of protection at Chipps Island and a day of 
protection at the Confluence is 12,276 AF/year. These estimates of the 
difference in water supply impact can be compared to the dollar value 
of that water, which the draft RIA estimates as being $90 per AF.

E. Regulatory Flexibility Act

    The Regulatory Flexibility Act, 5 U.S.C. Sec. 601, et seq., 
requires EPA and other federal agencies to prepare an initial 
regulatory flexibility analysis (IFRA). EPA's internal guidelines 
require that an IFRA include a profile of the small entities and 
determine if the statutory authority allows consideration of 
alternative implementation actions.
    EPA has determined that the action does not allow consideration of 
alternative implementation actions. First, under the Clean Water Act, 
water quality criteria must be based solely on science. Second, EPA is 
promulgating water quality criteria that in effect supplement state 
criteria that fail to meet the requirements of the CWA.
    EPA has prepared an abbreviated regulatory flexibility analysis. 
It's findings include the following:
     Minimizing the impacts on small farms can be accomplished 
by developing the least costly implementation plan, which distributes 
water supply reductions widely and facilitates trading between water 
districts. Given that allocation of water at the farm level depends 
primarily on decisions at the irrigation district level, determining 
which size farm would experience water supply impacts will also be 
difficult at the State level.

F. Availability of the Record

    The administrative record concerning the California Bay/Delta Water 
Quality Standards discussed in this preamble is available for public 
inspection and copying at the Environmental Protection Agency, Region 
IX Office, Water Quality Standards Branch, 75 Hawthorne Street, San 
Francisco, California 94105.

G. Specific Issues for Commenters to Address

    Written public comments are invited on all issues raised in this 
notice. EPA is especially interested in soliciting public comments on 
the following issues:
    1. EPA requests comments on the feasibility of setting water 
quality criteria based on a smooth function rather than on the mean 
value for each water year type categories.
    Testimony at recent State Board hearings criticized the use of 
water year type categories. Because water year types can change as the 
year progresses, criteria based on the historical mean for each water 
year type can cause major changes in project operations and habitat 
conditions if a given year shifts from one water year type to another. 
For example, a later season storm could cause the water year type to be 
reclassified from the below normal category to the above normal 
category. This shift would increase the number of required days of 
compliance at Chipps Island from 119 to 144 days. Such large and sudden 
changes are inefficient for water resource management and can harm 
aquatic resources by dewatering or washing away newly spawned eggs. One 
formulation of the criteria that could provide for more gradual shifts 
is described below.
    California DWR, USBR, and others have suggested that a smooth 
function should replace the use of means for each water year type 
category. Use of these smooth function equations would result in the 
same average number of days required for each year type but would 
involve higher numbers in wetter years within the category and lower 
numbers for the drier years within each category. Incorporation of a 
smooth function would likely ease the actual operational procedure to 
meet the criteria and would avoid the relatively large scale changes in 
operations that might come from a shift in the determination of year 
type as spring progresses.
    EPA has discussed the use of a smooth function criteria with water 
project operators and the State Board, and has thus far received a very 
positive response. Because it is a new approach that has not received 
substantial scrutiny in California, EPA's proposal above relies on the 
traditional water year type classification. However, if public comments 
do not raise any significant issues preventing its use, EPA would be 
inclined to use the smooth function criteria as an alternative to the 
water year type classification.
    The discussion below describes one possible approach to the 
construction of a smooth function criteria, and compares the potential 
effects of those functions with the traditional water year type 
criteria. Because no critically dry years occurred in the reference 
period it is necessary to extrapolate from the four year types for 
which there are data to the critical year type. Fortunately, there is a 
very high correlation among the four points (Figs. 1 and 2). These 
extrapolations allow the required number of days at Roe and Chipps 
Islands in each year type to be described as a pair of smooth 
functions.
    Port Chicago Equation (see Figure 1). Days=76 * Index-3.3 * 
(index)\2\-299
    This equation produces a wide range of required number of days 
within most year types and in all but wet years would involve a range 
of about thirty days. Use of the equation would result in little 
variance within wet years.

BILLING CODE 6560-50-P

TP06JA94.008


BILLING CODE 6560-50-C

------------------------------------------------------------------------
              Port Chicago (64 km)                 Mean     Min     Max 
------------------------------------------------------------------------
Wet.............................................     133     122     150
Above normal....................................     105      94     121
Below normal....................................      78      57      93
Dry.............................................      33      16      56
Critical........................................       0       0      15
------------------------------------------------------------------------
Figure 3.                                                               


    The relationship between number of days at Port Chicago and 
Sacramento Basin Index (Figure 3) yields differences of required number 
of days within year types of as much as 40 days in dry years. With the 
difference in flows required to sustain the isohaline at Port Chicago 
(29,000 cfs) and Chipps Island (12,000 cfs), the theoretical difference 
in water costs within a year type could be substantial. The actual 
costs are likely to be lower, however, because flows sufficient to 
trigger the standard are often followed by a considerable period of 
elevated flows sufficient to meet the required number of days. These 
differences are likely to be fully realized in dry and critical years 
when conditions in the Delta are fully controlled by the projects.

Chipps Island Equation (see figure 2)
    Days = 26.3 * Index - 1.13 * (index) - 4.6

    This equation results in small differences within each of the year 
types, with the exception of critical years.

BILLING CODE 6560-50-P

TP06JA94.009


BILLING CODE 6560-50-C

------------------------------------------------------------------------
              Chipps Island (74 km)                Mean     Min     Max 
------------------------------------------------------------------------
Wet.............................................     148     142     150
Above normal....................................     144     133     141
Below normal....................................     119     118     132
Dry.............................................     116     105     118
Critical........................................      90      66    104 
------------------------------------------------------------------------
Figure 4.                                                               


    The relationship between number of days at Chipps Island and 
Sacramento Basin Index (Figure 4) yields very small ranges about the 
mean for all but critical years. However, use of a smooth function is 
justified because of the open-ended nature of critical years. The 
driest year on record had a Sacramento Basin Index of 3.1, but the 
index theoretically could approach 0. This wide span of possible index 
values in the critical year type is best handled by the smooth function 
described. The smaller flows this standard entails (12,000 cfs at 
Chipps and 5,800 cfs at the confluence) and the small range of values 
within all but critical year types yields smaller differences in water 
costs.
    In summary, a smooth function to determine the number of days of 
compliance would result in the same average number of days for each 
year type, but would more accurately reflect differences within these 
categories. Hence, small adjustments could be made in project 
operations as the water year progresses.
    The use of a smooth function addresses, to some extent, the issue 
of adjusting habitat protection requirements in extended droughts. The 
present identification of year type is based on the Sacramento River 
Index. That index combines three variables: (1) Precipitation in the 
April through September period when flood control requirements are 
reduced and more precipitation can be held in reservoirs, (2) the index 
of the previous year which partly reflects the amount of carry-over 
storage, and (3) precipitation in the October through March period. The 
index weights these three factors in a 40:30:30 ratio. For the purpose 
of protecting estuarine habitat, the precipitation in February to June 
and the amount of carry-over storage may be more important than 
precipitation in the rest of the year. EPA is requesting comments on 
the possibility of modifying the Sacramento River Index for purposes of 
developing the salinity criteria as follows:
    (a) The criteria could calculate an index weighted more toward the 
previous year's Sacramento River Index and the February through June 
precipitation. A 40:40:20 ratio or even 50:50:0 index might be a more 
appropriate basis for the criteria.
    (b) The criteria could start each February with a baseline set of 
requirements and add or subtract days at each of the two downstream 
sites based on how conditions in each month differ from the average 
conditions for that month.
    2. EPA is including a 14 day rolling averaging period in its 
proposed salinity criteria. As discussed above, the 14 day period was 
included to assure that the range of spring to neap tidal conditions 
was included in the averaging period. Accounting for the effects of 
tidal influences is important, especially for the downstream compliance 
location at Roe Island. During its discussions of this proposal with 
the operators of California's major water projects, it was suggested 
that a 28 day rolling average or other averaging period may be more 
appropriate, so that the entire tidal cycle is included. EPA's 
preliminary review of this suggestion indicates that it would be an 
appropriate device for accounting for tidal influences, and would not 
have any detrimental impact on protecting the designated Estuarine 
Habitat use. Therefore, if public comments do not raise any significant 
issues, EPA would be inclined to use a 28 day averaging period. EPA, 
therefore, is requesting comments on the following alternative 
approaches to the averaging period:
    (a) The proposed criteria could be measured using a 28 day rolling 
average, thereby lengthening the averaging period to encompass the full 
range of tidal strengths and giving an overall effect of the tidal 
cycle.
    (b) The criteria could measure compliance with a rolling average 
but allow discontinuities in the averaging period. Thus, days on which 
meteorological conditions interfere with achieving the 2 ppt criteria 
at Roe Island would be counted instead as days of meeting the criteria 
upstream at Chipps Island. This approach could be applied only until 
all days that are required at the upstream site are met.
    3. As a part of EPA's coordination process in developing this 
proposal, the Agency has discussed its proposed criteria at length with 
the operators of California's major water projects. These operators, 
who will have substantial responsibilities under any implementation 
plan developed by the State Board, raised a question about how 
compliance with the 2 ppt salinity criteria should be measured. Under 
existing operational models, these operators would translate the 
proposed criteria into a set of flow parameters, and would operate the 
system pursuant to those flow parameters so as to achieve the 2 ppt 
salinity criteria at the targeted sites. However, because all models 
contain imperfections, it has been proposed that the operators should 
actually model compliance at a site somewhat downstream of the targeted 
site so as to provide a ``margin of error'' or a ``confidence 
interval''.
    EPA's preliminary review of this issue suggests that use of a 
``confidence interval'' of this kind is unwarranted, for two primary 
reasons. First, the model that predicts the location of the 2 ppt 
isohaline based on flows is extremely accurate. EPA's preliminary 
review of the model's accuracy during the five months covered by the 
proposed salinity criteria, using historical data, found that the model 
correctly predicts the number of days for the isohaline position more 
than 95 percent of the time. Second, the use of a 28 day averaging 
period, as described above, would adequately address most of the 
variability associated with factors not included in the salinity-flow 
model. For these reasons, EPA believes that the use of these proposed 
confidence intervals would require substantial additional flows through 
the estuary without any corresponding ecological benefit to the 
Estuarine Habitat designated use.
    EPA expects that the State Board will develop an implementation 
plan for these Estuarine Habitat criteria by changing the volume and 
timing of water flows through the estuary. EPA believes that an 
implementation plan that relies on the salinity-flow model, without 
making additional allowances for confidence intervals as described 
above, would be acceptable for purposes of protecting the designated 
use. Further, EPA notes that the State's triennial review provides a 
mechanism for regularly reviewing the adequacy of any implementation 
decisions concerning confidence intervals for the proposed salinity 
criteria.
    EPA solicits comment from the public on this issue, and welcomes 
any evaluation on the merits of the use of this or other forms of 
confidence intervals with the proposed criteria. Specifically, EPA 
requests comment on whether the proposed criteria without the above 
confidence interval adjustment would be protective. Alternatively, 
would a confidence interval based on an extended number of days of 
compliance at the targeted sites yield the desired level of confidence 
without requiring the higher flows required by the confidence interval 
proposal outlined above?
    4. Will these criteria be adequate to protect low-salinity habitat 
conditions in wetter years? The SFEP workshop that developed the 
scientific rationale for an estuarine index based their conclusions on 
correlations between mean position of the 2 ppt isohaline during 
appropriate months and the abundance of estuarine organisms at all 
trophic levels. With the exception of mollusks, yearly measures of 
abundance increase either linearly or logarithmically as the mean 
location of the 2 ppt isohaline moves down the estuary.
    EPA has developed its proposed Estuarine Habitat criteria based on 
the number of days at particular locations in the estuary, rather than 
a mean position over a series of months. These criteria have the 
advantage of being more easily implemented, and more directly tie 
certain salinity ranges to certain geographic locations (such as the 
extensive shallows of Grizzly Bay). However, basing the number of days 
on a certain historical period (such as 1940 to 1975) does not mean 
that the mean position of the 2 ppt isohaline for these reference years 
will be achieved. By using the historical period of 1940 to 1975 to 
define the number of days at each location, we are approximating the 
actual historical (late 1960's to early 1970's) mean position of the 2 
ppt isohaline in drier years. However, EPA's criteria may not provide 
overall conditions equal to those during the late 1960's to early 
1970's. This is because the mean position of the 2 ppt isohaline in 
wetter years has been substantially downstream of the wetter year 
positions in the proposed rule (see Table below). 

 Mean Position, in km, of the February Through June 2 ppt Isohaline, by 
   Year Type, for 1940-1975 Historical Period and Late 1960's to Early  
1970's Historical Period (Based on DAYFLOW Information and the Salinity/
 Flow Relationship Developed by Kimmerer and Monismith; SFEP 1993b), and
                              EPA Criteria                              
------------------------------------------------------------------------
           Year type                C       D       BN      AN       W  
------------------------------------------------------------------------
1940-1975.......................  ......      70      67      59      56
1964-1975.......................  ......      74      73      62      59
EPA criteria--with trigger\9\...      77      73      70      67      65
EPA criteria--without trigger...      77      76      75      74     74 
------------------------------------------------------------------------
\9\The EPA criteria include the Roe Island criteria with its            
  ``trigger'', which in some years will not be triggered. These two sets
  of results indicate the mean position of the 2 ppt isohaline in the   
  event that the Roe Island criteria is and is not triggered.           


    These wetter years are an important component of the natural 
hydrology; 40 percent of the last 50 years have been in the ``wet'' 
category. They are years of very high productivity for the estuary, and 
are likely to provide a buffer for times of low productivity, 
especially for those species living longer than one or two years. Such 
variability also encourages diversity, such as the plant diversity in 
brackish tidal marshes bordering Suisun Bay. While many of the winter/
spring flows during these years are presently considered 
``uncontrollable,'' a number of new water projects have been proposed 
that would capture part of these flows.
    One concern about the future development of these ``uncontrolled'' 
flows involves a possible decrease in the frequency with which 
triggering conditions will occur. The level of protection afforded by 
the Roe Island standard would be reduced if additional upstream water 
developments decrease uncontrolled wintertime flows, thus reducing the 
frequency with which the standard is triggered. EPA welcomes comments 
on how this standard should be modified to reflect future changes in 
upstream water development facilities.
    An additional concern about the protection of conditions in wetter 
years is that some wet years are much more productive than others. By 
developing standards that can be met in all wet years some of the 
biological values associated with exceptional years is not included. 
Part of the difficulty of developing criteria to protect the biological 
value of these wetter years arises from the open-ended nature of the 
wet year category. Recent wet years include years as different as 1983 
and 1986. In 1983, precipitation, both rain and snow, was heavy 
throughout the winter and spring. In 1986, on the other hand, a large 
tropical storm produced record-setting precipitation which lasted for a 
brief period and fell almost entirely as rain. Although both these were 
wet years, 1983 had about three times the amount of precipitation of 
1986 and, because of the heavy snowfall, a much higher amount of water 
was available for use. Possible ways to protect the value of wet year 
habitats include the use of triggered standards downstream of Roe 
Island or by requiring more days at Roe Island in the wettest years.
    EPA welcomes suggestions on the proper level of protection that 
should be provided during these wetter periods.
    5. One of the critical elements of EPA's proposal is the 
determination of the proper historical reference period for developing 
target numbers of days when the 2 ppt isohaline is at a particular 
point in the estuary. As discussed above, EPA is recommending a level 
of protection for the Bay/Delta similar to that existing during the 
late 1960's to early 1970's. To estimate the hydrological conditions 
during the late 1960's to early 1970's across the five water year 
categories, EPA is proposing using the 1940 to 1975 period as the 
historical reference period.
    The choice of years to include in the historical reference period 
can strongly affect the number of days when the 2 ppt isohaline is at a 
particular point. Incremental changes in the number of days have 
corresponding incremental effects on the water supply impacts of these 
proposals.
    Prior to the building of Shasta Dam, uncontrolled spring runoffs 
resulted in as many as 150 days when the 2 ppt isohaline was located at 
or below Chipps Island, even in critical years, whereas in recent years 
there have been as few as 0 days. In developing the proposed rule, EPA 
has used the period between October 1939 and September 1975 to 
represent the period when the conditions in the estuary were sufficient 
to protect the designated fisheries uses. As explained above, this span 
of years provides the greatest number of examples of each year type 
during the period after the massive changes in hydrology due to the 
construction of the Shasta Dam on the Sacramento River and the Friant 
Dam on the San Joaquin but before the most dramatic recent declines in 
fishery abundance. Even so, the chosen historical reference period 
contains no examples of critical years and only three examples of above 
normal years.
    One example of the variability of conditions within the chosen 
historical reference period involves the Chipps Island location. There 
is a great deal of variability in the number of days the 2 ppt 
isohaline was at Chipps Island within each of the drier year types in 
the historical reference period. Although the years with fewest days 
occurs later in the period there are examples of later years with more 
days than earlier years. The following table gives the number of days 
that the 2 ppt isohaline was west of Chipps Island for each dry and 
below normal year in the historical period. The latest examples of dry 
years in the proposed reference period, 1964 and 1961, had the fewest 
days at Chipps Island. These two dry years, however, were immediately 
preceded by a dry year (1960) with a number of days at Chipps Island 
substantially greater than the historical mean, and the year with the 
third lowest number of days at Chipps actually occurred in 1947. The 
absence of a strong pattern of decreasing days at Chipps Island over 
time was the principal basis for EPA's use of as broad a historical 
period as possible, the full period from 1940 to 1975, as the 
historical reference period.

------------------------------------------------------------------------
                                                        Dry      Below  
                       Year                           years      normal 
------------------------------------------------------------------------
Number of days between February and June when 2 ppt                     
 isohaline was west of Chipps Island;                                   
1930...............................................       146  .........
1932...............................................       151  .........
1935...............................................  ........        150
1936...............................................  ........        151
1937...............................................  ........        150
1939...............................................       106  .........
1944...............................................       142  .........
1945...............................................  ........        150
1946...............................................  ........        150
1947...............................................       111  .........
1948...............................................  ........        143
1949...............................................       141  .........
1950...............................................       150  .........
1955...............................................       129  .........
1957...............................................  ........        147
1959...............................................  ........         81
1960...............................................       123  .........
1961...............................................        89  .........
1962...............................................  ........        136
1964...............................................        75  .........
1966...............................................  ........        112
1968...............................................  ........         83
1972...............................................  ........         63
1979...............................................  ........        117
1981...............................................        76  .........
1985...............................................        31  .........
1987...............................................        46  .........
1989...............................................        39  .........
------------------------------------------------------------------------


    During the development of EPA's proposal, it has been suggested 
that the years 1964 to 1976 could be used as an alternative historical 
reference period. This period almost literally replicates the intended 
late 1960's to early 1970's. EPA has not chosen that period for two 
reasons. First, it is an extremely limited sample of the variation of 
conditions within water year categories. Second, including the year 
1976 is inappropriate, given that by 1976 the decline of certain 
aquatic resources was already apparent.
    Another suggested possibility is that use of the 1955 to 1975 time 
period may be a better indicator of conditions in the late 1960's to 
early 1970's. The 1955-1975 period excludes water years before the 
CVP's pumping facilities were operational, but still provides a larger 
sample across certain water year types than would using the 1965 to 
1974 period alone. As the table above indicates, using this 1955 to 
1975 period would decrease the number of Chipps Island days from 116 to 
approximately 104 days during dry years, and from 119 to approximately 
104 days during below normal years.
    EPA did not use this 1955-1975 period as the historical reference 
period because, as explained above, it believes the 1940 to 1975 period 
provides a larger and more representative sample of hydrological 
conditions across all year types similar to those in the late 1960's to 
early 1970's.
    Given the importance of this issue, EPA requests comments on the 
suitability of the above suggestions or of other historical reference 
periods for the salinity criteria. EPA is especially interested in how 
the use of alternative periods could provide a better estimate of the 
hydrological and ecological conditions in the estuary in the late 
1960's to early 1970's. In addition, EPA is soliciting comment on 
alternative approaches to developing reference conditions for water 
year types for which there are limited historical examples.
    6. During the spawning season, several species appear to be carried 
through the Delta to Suisun Bay during periods of elevated Delta flows 
caused by upstream storm events. The proposed Roe Island salinity 
criteria are partly intended to protect the normal dispersal of these 
young fish throughout Suisun Bay over a number of tidal cycles. As 
explained in more detail above, the proposed Roe Island criteria 
include a ``trigger'' that activates the criteria only after natural 
hydrological conditions push the 2 ppt isohaline to Roe Island. EPA is 
requesting comment on this trigger, including comment on the following 
specific questions:
    (a) Would a trigger at some upstream site, such as Middle Ground, 
retain the desired link to storm events while ensuring a more frequent 
triggering of the standard?
    (b) Should the criteria be triggered only by storm events actually 
occurring in the February through June period? This refinement would 
prevent the criteria from being triggered, for example, solely by a 
large storm occurring in January, the runoff from which may keep the 2 
ppt isohaline below Roe Island into February.
    (c) Should the trigger be stated as a single day when mean 
salinities are less than 2 ppt, or by a longer averaging period (14 
days, 28 days, etc.)?
    (d) It has been suggested that the need for a trigger might be 
eliminated by setting a criteria at a location further upstream. Both 
USFWS and USBR have suggested developing a criteria at Middle Ground 
(at roughly km 68). At this location the criteria would be triggered in 
all but critical years and would thereby provide an increased level of 
protection overall. Even though a Middle Ground criteria would require 
more days of protection than the Roe Island criteria, the upstream 
location means that the water supply impacts would be less than for the 
Roe Island criteria in years when the Roe Island criteria would have 
applied. It is likely that a shift of the downstream requirement from 
Roe Island to Middle Ground would have higher water supply impacts on 
average but lower impacts in particular years. At the same time, 
however, this shift in the downstream location would mean that the 
criteria would no longer be directly tied to salinities in San Pablo 
Bay that have been identified as biologically important for starry 
flounder, longfin smelt, and the shrimp, Crangon franciscorum.
    7. Several participants in the State Board hearings stressed the 
importance of avoiding consecutive years of poor habitat conditions for 
short-lived species, such as Delta smelt and longfin smelt. For 
example, Dr. Moyle recommended that relaxations of the Roe Island 
standards to Chipps Island during dry and critical years be limited to 
two consecutive years. Similarly, during the course of the Agency's 
discussions with USFWS and NMFS about the potential effects of these 
proposed criteria on threatened and endangered species, a question was 
raised about whether the proposed criteria would adequately protect the 
listed Delta smelt in an extended drought. Recent extended droughts in 
the Bay/Delta watershed have lasted six or seven years, but there is 
scientific evidence that droughts as long as fifty years have occurred 
and could happen again. Although droughts of this magnitude are 
unlikely, such a drought would have serious adverse impacts on the 
estuary's fisheries resources, and especially on fishes with short life 
cycles such as the Delta smelt.
    At the same time, water project operators have suggested that 
extended droughts impose special constraints on project operations and 
deliveries, and have recommended that EPA propose relaxations of the 
Estuarine Habitat criteria during extended droughts.
    EPA is soliciting comments on whether it is necessary to promulgate 
special criteria to deal with the issue of consecutive dry or critical 
years or extended drought. EPA is particularly interested in comments 
on the biological requirements of threatened and endangered fishes 
during these periods, and on the operational impacts of special 
protection measures during these periods.
    8. In this proposed rule, EPA is relying on the Estuarine Habitat 
criteria to protect the tidal wetlands bordering Suisun Bay. Tidal 
wetlands provide habitat for diverse marsh, aquatic and wildlife 
species, as well as special status species such as the Suisun song 
sparrow, Delta tule pea, black rail, clapper rail and soft-haired 
bird's beak. EPA's proposed criteria have been developed to protect 
aquatic species and to provide salinity conditions similar to those in 
the late 1960's to early 1970's. Therefore, many of the aquatic species 
that inhabit the marsh channels should be better protected under our 
proposed criteria. In addition, the proposed Estuarine Habitat criteria 
are designed to provide substantially better dry and critically dry 
year springtime conditions than the recent year conditions that have 
caused adverse effects on the tidal marsh communities bordering Suisun 
Bay. EPA therefore believes that these criteria will provide 
substantially better conditions in the marshes, but is soliciting 
comment as to whether additional criteria are necessary to fully 
protect the marsh resources.
    Although EPA does not believe that there is a sufficient scientific 
record at this time to establish specific numerical salinity criteria 
for the tidal wetlands, it may be possible to set narrative criteria 
which could be developed into numerical criteria in the near future as 
additional information becomes available. To be consistent with EPA 
guidance, such narrative criteria should include specific language 
about conditions that must exist to protect a designated use, and must 
be quantifiable so that numeric standards can be developed (USEPA, 
1990). Examples of possible narrative criteria for the Suisun Marsh 
are:
    (1) ``Water quality conditions sufficient to support high plant 
diversity and diverse wildlife habitat throughout all elevations of the 
tidal marshes bordering Suisun Bay''
    (2) ``Water quality conditions sufficient to assure survival and 
growth of brackish marsh plants dependent on soils low in salt content 
(especially Scirpus californicus and Scirpus acutus) in sufficient 
numbers to support Suisun song sparrow habitat in shoreline marshes and 
interior marsh channel margins bordering Suisun Bay.''
    EPA welcomes any information or recommendations on criteria to 
protect the Suisun Bay tidal marshes.
    9. USFWS and NMFS have expressed concern that special measures may 
be necessary to protect Delta smelt in the event of a late spawn. In 
particular, these agencies have suggested that if real-time monitoring 
indicates that peak Delta smelt spawning occurs in late June or July, 
it might be appropriate to maintain the 2 ppt isohaline in Suisun Bay 
during those months to assure that juveniles remain in the suitable 
rearing habitat in eastern Suisun Bay.
    EPA is soliciting comment as to whether and how these measures 
should be incorporated into water quality criteria, and on the 
operational impacts of such criteria. In addition, EPA requests comment 
on how implementation of these criteria would affect carryover storage 
requirements presently imposed on water projects for the benefit of the 
threatened winter-run Chinook salmon.
    10. EPA is proposing salmon smolt survival criteria to protect the 
Cold Fresh-Water Habitat and Fish Migration designated uses. These 
criteria would address EPA's concerns with certain temperature criteria 
contained in the 1991 Bay/Delta Plan that were disapproved by EPA. As 
explained in more detail above, the Agency believes that it presently 
has an inadequate basis to propose temperature criteria. Further, the 
adoption of salmon smolt criteria provides the State with more 
flexibility in determining an implementation plan protecting the 
fisheries use.
    EPA is soliciting comment as to whether an adequate scientific 
basis exists to propose a temperature criteria alone. The Agency is 
especially interested in receiving comment as to whether a temperature 
criteria would provide better protection for the designated uses than 
the proposed criteria, and whether a temperature criteria could be 
implemented given the present operational flexibility in the estuary.
    11. EPA welcomes any additional information on the effectiveness 
and feasibility of installing a barrier to fish (including a sound 
barrier) at the head of Georgiana Slough. Results from USFWS coded-wire 
salmon smolt experiments clearly demonstrate that migrating smolts 
survive poorly in the central Delta, and salmon smolt survival would be 
higher if fish migrated down the main Sacramento River channel. Closure 
of Georgiana Slough is one of the implementation measures that the 
Delta Team of the Five Agency Chinook Salmon Committee evaluated and 
recommended as a measure to increase salmon smolt survival, and 
survival indices recommended by the fisheries agencies included this 
measure. The major concerns over Georgiana Slough closure are: 
exacerbation of the reverse flow situation in the lower San Joaquin 
River, degradation of water quality conditions in the Central Delta, 
and blocking of upstream migration of adult salmon. It is likely that 
reverse flows would become less of a problem with a barrier in place in 
Georgiana Slough if exports were balanced with San Joaquin River flows 
to continue to provide positive flows in the lower San Joaquin. EPA 
would like more information on whether a balance could be achieved to 
provide some periods of time when a Georgiana Slough barrier would be 
beneficial for salmon without causing detrimental effects on the other 
species and habitats in the Delta. Since EPA's proposed salmon smolt 
survival index is a criteria to protect the outmigration of smolts, and 
Georgiana Slough closure is a measure that would be beneficial for 
outmigrating salmon, EPA solicits comments on whether the target index 
values in its proposal should be changed.
    12. As explained in more detail above, EPA has based its proposed 
index values for the salmon smolt survival criteria for the San Joaquin 
River on recommendations by the USFWS, NMFS and California DFG at the 
State Board's Interim Water Rights Hearings for the San Francisco Bay/
Sacramento-San Joaquin Delta Estuary. These recommendations include 
placing a barrier at the head of Old River during migration of San 
Joaquin River system smolts through the Delta (April 1 until May 31). 
The Old River barrier was also recommended by the Delta Team of the 
Five Agency Chinook Salmon Committee, and is one of the projects called 
for in the CVP Improvement Act. However, discussions with USWFS and 
NMFS carried out during EPA's consultations under the ESA have raised 
questions about whether the barrier would adversely affect reverse 
flows in the central Delta under certain conditions. EPA is therefore 
requesting comment on the following issues:
    (a) Would the proposed salmon smolt criteria index values on the 
San Joaquin need to be revised if the Old River barrier is not built? 
In what ways?
    (b) Should EPA promulgate alternative or additional criteria that 
would be effective in the event that the Old River barrier is not 
constructed?
    13. In addition to a barrier at the head of Old River, the USFWS 
implementation recommendations for the San Joaquin also included 
certain export limits and flow requirements during peak migration 
periods. Export limits are also an important measure for achieving 
protection for migrating smolts on the Sacramento River system, 
especially if there is no barrier in place at Georgiana Slough, and are 
an element of the models used to generate the salmon smolt survival 
indices on the Sacramento River. EPA is concerned that there may be 
implementation scenarios for the two rivers that could result in 
detrimental conditions for migrating smolts even if the proposed index 
values are achieved. One such possible scenario may occur if the State 
Board adopts USFWS implementation recommendations on the Sacramento 
River (adjusted, as described above, to account for Georgiana Slough 
remaining open), but then operates the San Joaquin River so as to just 
meet the proposed index values. In this case, our preliminary review 
indicates that the San Joaquin River index value theoretically might be 
attained with lower flows than are protective for the salmon resources. 
The USFWS has substantial evidence that San Joaquin River flows are a 
critical element for successful smolt migration. Protection of 
migration for these runs is particularly important considering the low 
abundances and poor conditions in the San Joaquin system.
    The discussion above raises the possibility that the salmon smolt 
criteria for the San Joaquin River system may need to be refined. We 
are therefore requesting comment as to whether the proposed index 
values should be revised to reflect the interrelation between 
Sacramento River and San Joaquin River implementation measures 
recommended by USFWS. In particular, should the proposed index values 
be revised to account for the possible effects of low flow scenarios on 
the San Joaquin River?
    14. The Central Valley Project Improvement Act requires that 
measures be taken to double the production of anadromous fish species 
throughout the Central Valley watershed. EPA intends that its proposed 
criteria should support this goal in the waters of the Bay/Delta 
estuary. EPA appreciates any information on whether the proposed 
criteria provide the necessary protection to reach this goal.
    15. Dr. Wim Kimmerer has developed a salmon population model for 
the Sacramento River Basin, CPOP, which includes a regression model for 
the Delta based on the same USFWS data used to develop EPA's proposed 
criteria (BioSystems Analysis, 1989). This model is not divided into 
reaches, and uses all coded wire tag data from both ocean and trawl 
recoveries. Significant independent variables include: proportion of 
flow remaining in Sacramento River, flow in the Sacramento River, the 
interaction between these two, and temperature at Freeport. Dr. 
Kimmerer compares his analysis with the USFWS analysis, and reports 
that his analysis outperforms the USFWS analysis and, in addition, that 
it better models temperature effects on mortality. However, this model 
uses only pre-1989 data. EPA appreciates any comments on the usefulness 
of this model in predicting Sacramento River smolt survival and setting 
criteria to protect Fish Migration as a designated use.
    16. A number of species in the Bay/Delta estuary appear to rely on 
estuarine conditions during the months of July to January. These 
species include herring (primarily a Bay species), late fall-run 
salmon, and juvenile striped bass. EPA welcomes any information on 
habitat conditions necessary for protection of these species, and on 
possible revisions to the proposed criteria that could address these 
species.
    17. EPA is concerned that changes in water project operations in 
response to the proposed criteria may have unforeseen environmental 
impacts. EPA welcomes comments as to whether there are any operational 
scenarios for the CVP, SWP, and/or other water users that would 
increase or decrease the ecological benefits of the proposed criteria. 
In addition, EPA notes that, under the CWA, the state will conduct 
triennial reviews of these and other water quality criteria to 
determine whether they are adequate to protect the designated uses. At 
those times, the state has the opportunity to adjust criteria that are 
shown to be over or under protective of the uses. EPA welcomes comments 
as to the kinds of information, such as biological resource monitoring 
data, that are or will be available to measure the effectiveness of 
fish and wildlife criteria in the Bay/Delta.

List of Subjects in 40 CFR Part 131

    Environmental protection, Water pollution control, Water quality 
standards, Water quality criteria.

    Dated: December 13, 1993.
Carol M. Browner,
Administrator.

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Sacramento-San Joaquin Delta Estuary, DFG Delta Fish and Wildlife 
Protection Report 8 pages 36-43.
Turner, J.L. and H.K. Chadwick, 1972. Distribution and abundance of 
young-of-year striped bass (Morone saxatilis) in relation to river 
flow in the Sacramento-San Joaquin Estuary. Transactions American 
Fisheries Society 101(3):442-452.
USBR, 1991. Executive summary 1990 striped bass egg and larvae 
management studies San Francisco Bay-Delta estuary. Bureau of 
Reclamation, Sacramento, California, 18 pp. WRINT-USBR-2.
USEPA, 1990. Biological Criteria: National Program Guidance for 
Surface Waters. EPA-440/5-90-004, April 1990.
USFWS, 1987. The needs of chinook salmon, Oncorhynchus tshawytscha 
in the Sacramento-San Joaquin Estuary. Prepared for the SWRCB 1987 
Water Quality/Water Rights Proceeding on the San Francisco Bay/
Sacramento-San Joaquin Delta. USFWS Exhibit 31.
USFWS, 1992a. Measures to improve the protection of chinook salmon 
in the Sacramento/San Joaquin River Delta. WRINT-USFWS-7. Expert 
testimony of U.S. Fish and Wildlife Service on chinook salmon 
technical information for State Water Resources Control Board Water 
Rights Phase of the Bay/Delta Proceedings, July 6, 1992.
USFWS, 1992b. Abundance and survival of juvenile chinook salmon in 
the Sacramento-San Joaquin Estuary. 1991 Annual Progress Report. 
Sacramento-San Joaquin Estuary Fishery Resource Office, U.S. Fish 
and Wildlife Service, Stockton, Calif. June, 1992.
USFWS, 1992c. Expert testimony of United States Fish and Wildlife 
Service on recommendations for interim protection and response to 
hearing notice key issues for State Water Resources Control Board 
Water Rights Phase of the Bay-Delta Estuary Proceedings. July 6, 
1992. WRINT-USFWS-8.
USFWS, 1992d. Delta Smelt Work Group Conclusions. 2 pp. 1992. WRINT-
USFWS-19.
USFWS, 1992e. Delta Smelt Work Group Scenarios. 2 pp. 1992. WRINT-
USFWS-20.
USFWS, 1992f. Notice of Review, Endangered and Threatened Wildlife 
and Plants. 54 FR 554-56 (January 6, 1989), also in WRINT-USFWS-15.
USFWS, 1992g. Interagency Statement of Principles, EPA, USFWS, and 
NMFS. 4 pp. 1992. WRINT-USFWS-10.
USFWS, 1993. Abundance and Survival of Juvenile Chinook Salmon in 
the Sacramento-San Joaquin Estuary. 1992 Annual Progress Report. 
Sacramento-San Joaquin Estuary Fishery Resource Office, U.S. Fish 
and Wildlife Service, Stockton, Calif. June 1993.
Wang, J.C.S., 1986. Fishes of the Sacramento-San Joaquin estuary and 
adjacent waters, California: a guide to the early life histories. 
Interagency Ecological Studies Program, Technical Report 9.
White, J.R. 1986. The striped bass sport fishery is the Sacramento-
San Joaquin Estuary, 1969-1979. California Fish and Game 72:17-37.

Appendix I to the Preamble--Managing Freshwater Discharge to the San 
Francisco Bay/Sacramento-San Joaquin Delta Estuary: The Scientific 
Basis for an Estuarine Standard (San Francisco Estuary Project, 1993) 
(Excerpts)

Introduction

    Aquatic resources of the Sacramento-San Joaquin Delta and upper 
portions of San Francisco Bay have undergone significant declines over 
the past several decades. Species characteristic of the Delta and 
rivers, such as striped bass and salmon, began to decline during the 
late 1970s. Prolonged drought, large diversions of fresh water, and 
dramatic increases in populations of introduced aquatic species during 
the 1980s and 1990s brought a number of indigenous aquatic species to 
extremely low levels. Species that spend more of their lives downstream 
of the Delta, including Delta smelt, longfin smelt, and many 
zooplankton, maintained large populations through the 1970s, but 
declined sharply after the mid-1980s. Declines in aquatic resources 
have led to curtailed fishing seasons, to petitions for endangered 
species status, and general concern about the health of the estuarine 
ecosystem.
    Concern over the impacts of increased salinity produced from the 
combination of drought and high diversion rates is not limited to 
aquatic communities. The few remaining fragments of brackish and 
freshwater tidal marshlands are particularly vulnerable to increased 
salinity or to reduced variability in salinity. Under natural 
conditions, these tidal marsh communities would move upstream with the 
changing salinity. But the flood plains and other lowlands suitable for 
the evolution of tidal marshes are absent upstream. Tidal marshes 
provide important habitat for numerous plants and animals of special 
concern.
    Large demands for water by the agricultural community and by 
California's burgeoning urban areas make it difficult to allocate 
additional freshwater for the protection of dwindling aquatic and 
wetland resources of the estuary. Management of the State's water 
resources necessitates a delicate balancing of needs, given the intense 
and growing competition for water. If the freshwater needs of the 
estuary are to be considered seriously they must be based on sensitive, 
straightforward, and diagnostic indicators of the responses of the 
estuarine ecosystem to patterns of freshwater inflow.
    An extensive body of scientific evidence indicates that flows into, 
within, and through the estuary are extremely important to organisms 
that depend on the estuary for at least a portion of their life cycles. 
However, the mechanisms by which flows affect different elements of the 
ecosystem are not well understood. In the Bay/Delta Estuary, many 
chemical and physical properties and processes are tightly linked to 
flow, including proportion of water diverted, salinity at a given 
point, the longitudinal position of a particular salinity range, and 
alteration of the effects of toxicants through dilutions. Any of these 
phenomena could be controlling a particular species, but each will also 
vary with the other variables that are closely correlated with flow.
    At present, the complex configuration of the Delta and the estuary, 
combined with the complex withdrawal and diversion network, preclude 
any simple, directly monitored measure of freshwater discharge to the 
estuary. Effective protection and management of the estuary requires an 
index of the estuary's response to freshwater inflow that (1) Can be 
measured accurately, easily and inexpensively; (2) has ecological 
significance; and (3) has meaning for nonspecialists. Net Delta 
outflow, which is calculated from various measures and estimates of 
water inflow and use, has been a useful tool but it does not satisfy 
all of these requirements. Because of the high correlations among the 
flow-related variables, the choice of a suitable index does not need to 
be based on any presumed mechanism.
    The San Francisco Estuary Project convened a series of technical 
workshops to evaluate the responses of estuarine biota and habitats to 
various conditions of salinity and flow. The workshops involved 
approximately 30 scientists and policy makers with expertise in 
estuarine oceanography and ecology, and in water and living resource 
management. The group focused its attention on the Suisun Bay area, the 
portion of the estuary downstream of the confluence of the Sacramento 
and San Joaquin rivers and upstream of Carquinez Strait. Internal Delta 
issues (such as gate closures, water exports, and internal flows) or 
problems of downstream portions of the San Francisco Bay (such as urban 
and industrial discharges) were not directly addressed by the group. No 
attempt was made to incorporate all management actions that might 
benefit biological communities, nor to identify what level of 
environmental restoration and protection should be set based on 
salinity and flow.
    Identification of freshwater needs of aquatic resources has caused 
conflict for a variety of reasons. Debate of scientific issues is 
fundamentally different from other kinds of debate in that it should 
yield to scientific investigation. Participants developed issue papers 
that delineated areas of scientific agreement. Several issue papers 
showed that conditions in Suisun Bay largely reflected the abundance, 
recruitment, or survival not only of local species, but also of habitat 
conditions for species upstream and downstream. A primary result of the 
issue papers produced for this group was that almost all species 
studied increased in abundance as a simple function of increased 
outflow and decreased salinity. The absence of a plateau or peak in the 
relationship of species abundances and outflow conditions means that 
science alone cannot identify an optimal outflow. Furthermore, the 
similar response of species at all ecological (trophic) levels argues 
strongly that the estuary should be managed using an ecosystem approach 
rather than on a species by species basis.
    The technical workshops concentrated on developing the scientific 
rationale for an estuarine index to measure the estuary's response to 
different levels and patterns of freshwater input. Participants 
recognized that economic and socio-political considerations should be 
accounted for at other points in the deliberations. The needs of 
society, as well as the needs of the environment, should be considered 
in determining appropriate allocations of freshwater. However, the 
premise of the workshops was that one should start with the best 
scientific and technical judgements possible.
    Many large-scale changes in the structure of the Delta have been 
proposed to facilitate water use and to reduce impacts of water 
withdrawal on aquatic resources. There was general recognition by the 
group that the present Delta withdrawal and distribution system is a 
major contributor to the declines of important species. The conclusion 
and recommendations of the workshops are based upon the present water 
withdrawal and distribution system and would need to be re-evaluated if 
any significant alterations to that system are considered.
    The conclusions and recommendations in this report were developed 
by the estuarine scientists and managers who participated in one or 
more of the workshops. The complete list of participants and their 
affiliations are listed in Appendix D. All conclusions and 
recommendations in this report were reviewed, voted on, and endorsed by 
a consensus of the estuarine scientists and managers who participated 
in the fourth and final workshop in the series (26 August 1992). The 
term consensus is used to represent group solidarity on an issue; a 
judgement arrived at by most of the scientists and managers present. In 
all cases, the consensus was unanimous or nearly unanimous. The 
conclusions and recommendations are arranged in a sequence that 
``tracks'' the evolution of thinking of the participants. The 
conclusions and recommendations reached by the group reflect the 
participants' best scientific and technical judgements, not necessarily 
the positions of their affiliated agencies or organizations.
    The following conclusions and recommendations are intended to 
provide guidance and information on how estuarine standards could be 
developed and how different levels of protection of estuarine resources 
could be selected.
    The full justifications to these conclusions and recommendations 
are contained in technical papers that accompany this report and in 
other documents prepared for the San Francisco Estuary Project. 
(Appendix E).

Important Conclusions and Recommendations

(1) Conclusion

    Because of the complex nature of the freshwater delivery and 
distribution system in the San Francisco Bay/Sacramento-San Joaquin 
Delta estuary, there is at present no single, simple, accurate measure 
of freshwater input to the estuary that conveys information important 
to resource managers and to the public, and that is meaningful to those 
with special concerns about how fluctuations in freshwater inflow to 
the estuary affect habitat and the condition of the estuarine 
ecosystem.

Recommendation

    Estuarine standards should be developed to be used in conjunction 
with flow standards. One set of standards should be based upon an index 
of the physical response of the estuary to fluctuations in the input of 
fresh water. These standards should have diagnostic value in providing, 
throughout the year, a level of protection to the estuary and to 
important ecosystem values and functions consistent with environmental 
goals and objectives for the Bay-Delta estuary.

(2) Conclusion

    Estuarine standards to be used in conjunction with flow standards 
should be based upon an index that is simple and inexpensive to measure 
accurately, that has ecological significance, that integrates a number 
of important estuarine properties and processes, and that is meaningful 
to a large number of constituencies.

Recommendation

    Salinity should be used as an index for the development of some 
estuarine standards.

Justification

    In the first workshop (August 1991), participants identified and 
assessed a number of indices of the estuary's responses to flow to use 
in managing freshwater discharge to the estuary. The preliminary, 
preworkshop, choice was the position of the entrapment zone. This index 
was abandoned quickly, however. The entrapment zone is important to 
estuarine ecosystem processes and functions, but at present there is no 
single, straightforward ``entrapment zone index'' suitable for 
monitoring the position or strength of the entrapment zone as a 
function of freshwater input.
    Salinity was selected as the most appropriate index because: (1) 
The salinity distribution is of direct ecological importance to many 
species; (2) the salinity distribution is a result of the interplay of 
freshwater input, geometry of the estuarine basin, diversion of fresh 
water in the Delta, and the tidal regime; and (3) salinity measurements 
can be made accurately, directly, easily, and economically. Moreover, 
since most of the major concerns about reductions in the freshwater 
input to the estuary are associated either directly or indirectly with 
the loss or alteration of low salinity habitat, salinity is an ideal 
index for keeping track of the extent--both area and volume--of low 
salinity habitat. The salinity distribution represents the response of 
the estuary to different combinations of river discharge, diversions 
and withdrawals, tidal regime, and basin geometry.

(3) Conclusion

    Salinity measured at about 1m above the bottom1 is an index 
upon which estuarine standards should be developed. The index is a 
practical way of tracking changes in habitat.
---------------------------------------------------------------------------

    \1\Because the difference between surface and near-bottom 
salinities is small and because the relationship between them is 
reasonably well known, surface salinity could also be used. Near-
bottom salinity is recommended, however, because it is a more stable 
indicator.
---------------------------------------------------------------------------

Recommendation

    Standards should be developed using an index that establishes an 
upstream limit of the position of the 2 near-bottom 
isohaline, averaged over different periods of the year.

(4) Conclusion

    Analysis of the available historical data indicates that, 
throughout the year, the farther downstream the 2 near-bottom 
isohaline is displaced, the greater the abundance or survival of most 
species examined.

Recommendation

    The downstream position of the 2 isohaline should be 
unconstrained.

Justification

    From the environmental perspective--an important perspective, but 
not the only one--scientific uncertainty dictates taking an 
environmentally conservative approach, i.e. providing enough Delta 
outflow to the estuary to push the 2 isohaline farther 
downstream than might be required with greater scientific certainty. It 
is anticipated, and preliminary analysis supports it, that the salinity 
standard--the upstream limit of the 2 near-bottom isohaline--
will vary from season to season to provide the desired level of 
protection.

(5) Conclusion

    Estuarine systems are characterized not only by short-term 
responses to the mean salinity at any given location, but also by 
responses to longer-term seasonal, annual and interannual variability 
in salinity and other properties.
    Recent advances in scientific understanding indicate that this 
dynamic character of healthy estuarine ecosystems is particularly true 
for the distribution and abundance of wetland vegetation, but also 
holds for other aquatic organisms.

Recommendation

    The potential importance of variations in salinity on different 
time scales to the structure and dynamics of estuarine ecosystems 
should be considered in developing salinity standards. Deviations from 
the patterns of salinity variability in the historical data set could 
increase the risk of not achieving environmental goals and objectives 
even if mean positions of the 2 near-bottom isohaline were 
matched with the historical data sets.

Justification

    There is strong biological evidence from a number of estuaries 
throughout the world that variability in flow, in circulation and 
mixing, in the salinity distribution, and in the distribution of other 
important properties and processes is important in maintaining a 
healthy estuarine ecosystem. Therefore, variability in flow above the 
threshold needed to meet the seasonal salinity standard is encouraged.

(6) Conclusions

    Empirical statistical relationships were developed between a 
variety of estuarine properties and resources, and the position of the 
near-bottom 2 isohaline and other flow-related variables. The 
relationships developed are statistical relationships. They are not 
proof of cause-effect. The relationships indicate clearly, however, 
that the position of the near-bottom 2 isohaline can serve as 
a powerful diagnostic indicator of the condition of biological 
``units'' (communities, populations) across a range of different 
trophic levels.
    With the information these relationships can provide, water 
managers will be in a far better position to regulate freshwater 
discharge to the estuarine system to produce, on the average,2 
predictable and desirable ecological responses of the estuary 
consistent with goals selected for the estuarine ecosystem. If this 
strategy is followed, the probability of the desired ecological 
response will be enhanced and the chances of undesirable ecological 
surprises in the estuary will be reduced.
---------------------------------------------------------------------------

    \2\Over a period of several years.
---------------------------------------------------------------------------

    Because the statistical relationship between net Delta outflow and 
the position of the near-bottom 2 isohaline is strong, the 
position of the near-bottom 2 isohaline is an excellent 
surrogate for net Delta outflow in managing freshwater input to the 
estuary. The relationship may be improved further through routine 
direct monitoring of the position of the 2 isohaline and a 
suite of biological responses.

Recommendation

    The salinity distribution should be monitored continuously at a 
series of at least six stations spaced approximately five kilometers 
apart and located along the channel between about Emmaton and Carquinez 
Bridge. Measurements should be made at least near the surface and near 
the bottom at each station. The data should be telemetered to a 
convenient location for timely analysis and interpretation. These 
continuous monitoring data should be supplemented with detailed surveys 
to map the distribution of salinity in three dimensions. The data 
should be readily available in a timely way to all interested parties.
    An appropriate biological monitoring program should determine 
responses of a variety of organisms to changes in position of the 
2 isohaline.

Justification

    During the second and third workshops, and during intersessions 
between workshops, a systematic search was made to select the most 
powerful tools of analysis to describe how diagnostic biological 
indicators respond to changes in position of the near-bottom 
2 isohaline. When data were rich enough, other variables were 
included in the analyses.
    The first task was to specify the most diagnostic resource 
variables--the responses of indicators that would convey the maximum 
amount of environmental/ecological information. In every case, the 
objective was to demonstrate how these diagnostic environmental/
ecological indicators responded to changes in the position of the near-
bottom 2 isohaline and to a variety of other flow measures. 
In every case, experts on the particular biological response were 
consulted in selecting the appropriate averaging time for the position 
of the 2 isohaline.

(7) Conclusion

    The position of the near-bottom 2 salinity isohaline is 
an index of habitat conditions for estuarine resources at all trophic 
levels, including the supply of organic matter to the food web of 
Suisun Bay, an important nursery area. In other words, well-behaved 
statistical relationships exist between the near-bottom 2 
isohaline and many estuarine resources for which sufficient data exist 
to make appropriate analyses. Moreover, at least a rudimentary 
understanding exists for the causal mechanisms underlying many of these 
relationships. The location of the near-bottom 2 isohaline is 
important either because it is a direct causal factor or because it is 
highly correlated with a direct causal factor (e.g., diversions).
    Preliminary analyses show that errors in prediction using models 
which incorporate only the position of the 2 isohaline are 
comparable to the errors using more complex models which incorporate 
additional flow-related variables. In other words, given the present 
data sets, predictive models using only the position of the near-bottom 
2 isohaline perform as well as more complex models that 
incorporate other variables. However, some of these other variables may 
be very important in affecting habitat and the condition of biological 
resources of the estuary.

Recommendations

    At this time, the most appropriate basis for setting salinity 
standards for the portion of the estuary on which this report 
concentrates is the position of the near-bottom 2 isohaline 
alone, unless it can be shown either that another variable is the 
controlling variable or that incorporation of additional variables 
improves the predictive capability. Further research should be 
conducted to improve prediction of the responses of important estuarine 
resources to variations in the position of the near-bottom 2 
isohaline. That research should incorporate other variables where they 
can be shown to contribute significantly.

(8) Conclusion

    A number of key species are subject not only to the biological 
effects of the location of the near-bottom 2 isohaline, and 
therefore the effects of freshwater inflow to the estuary, but also to 
the physical effects of entrainment and diversion by the various water 
projects.

Recommendations

    Salinity standards should be keyed to the existing city, county, 
regional, state, and federal water diversion and distribution system. 
Proposed changes to that system should trigger a re-evaluation of the 
salinity standards to ensure that they will continue to provide the 
desired level of environmental protection while retaining as much 
flexibility as possible in meeting the state's other needs for water.
    Since a broad class of models can be constructed, including 
mechanistic and statistical models that incorporate both biological and 
physical parameters and other factors such as diversions, exports, and 
antecedent conditions, efforts should be enhanced to ensure a 
consistent, long-term accurate measurement program to enhance these 
models and to decrease the uncertainties in their application. The 
ultimate goal is to have a predictive model that incorporates the 
position of the 2 isohaline and other appropriate physical 
and biological variables.

(9) Conclusion

    Salinity standards should be based upon the best scientific and 
technical knowledge. A method is needed to summarize and to advance the 
state of scientific and technical knowledge of the complex 
relationships between variations in the position of the near-bottom 
2 isohaline during different periods of the year (and 
associated Delta outflow) and a variety of diagnostic ecosystem 
responses.

Recommendation

    Salinity and flow-response matrices should be developed for 
different biologically important periods of the year. The matrices 
should summarize the existing state of knowledge of the responses of a 
rich variety of estuarine organisms and communities as well as 
estuarine properties and processes, to the location of the near-bottom 
2 isohaline and associated freshwater discharge to the 
estuary. The estuarine properties and biological responses initially 
identified for inclusion in these matrices are summarized in Exhibit A.
    A Matrix Manager should be appointed to oversee the development of 
the summary matrices and to ensure quality control. The Matrix Manager 
should orchestrate the analyses of relevant data and ensure that the 
results of the analyses are cast into forms appropriate for the 
intended uses.
    Because estuarine habitat suitability and, therefore, estuarine 
ecosystem health are not simply a function of the instantaneous 
salinity distribution, the entry in each response cell of the matrix, 
whenever possible, should be based upon the development of functional 
relationships of estuarine properties to isohaline positions (and 
freshwater input to the estuary) that incorporate lagged terms, 
seasonal variability, and other water management variables. Ideally, 
the input to each matrix cell would include a directory of the 
appropriate model, or models, that could be used for prediction.
    The proposed matrices are shorthand methods for keeping track of 
advances in the state of scientific knowledge and for ensuring that the 
most up-to-date scientific knowledge is used in decision-making. They 
are not intended to be used as isolated regulatory tools. They are a 
summary of the state of development of those tools, a guide to which 
tools to use during different times of the year, and an index of where 
to find them. The responsibility for development of the matrices and 
for periodically updating them should be institutionalized. One 
appropriate agency might be the Interagency Ecological Studies Program.

Justification

    The proposed matrices are an effective shorthand way of summarizing 
in a convenient format the status of a large amount of data and 
information relating the responses of the estuary to fluctuations in 
freshwater inflow and to other water management variables. The matrices 
are a useful vehicle for summarizing the biological benefits--using a 
broad array of response indicators--of positioning the near-bottom 
2 salinity isohaline at various distances upstream (inland) 
from the Golden Gate Bridge during different periods of the year. The 
proposed matrices would provide the first quantitative and 
comprehensive summary of how the San Francisco Bay/Sacramento-San 
Joaquin Delta estuary ecosystem responds to fluctuations in freshwater 
inflow to the estuary (Delta outflow) and to the estuary's changing 
salinity regime. The matrices have further advantages. They will 
provide managers, policy-makers and the public with: (1) a clear 
statement by the scientific community of the current status of 
understanding of the effects of different freshwater discharge-
diversion scenarios on the estuarine ecosystem; (2) an identification 
of critical gaps in scientific knowledge that can be used to guide 
future research and monitoring activities; and (3) a summary that is 
easily updated on a cell-by-cell basis as new knowledge is developed.
    The models upon which the matrices are based can serve as tools for 
regulatory agencies to use in incorporating the environmental needs of 
the estuary into a set of management prescriptions for storing, 
releasing, and diverting water for consumptive uses. Section of the 
level or degree of biological response to be achieved--the level of 
environmental protection--is the responsibility of regulatory bodies 
acting in response to society's priorities.

(10) Conclusion

    The actual setting of salinity standards--specifying the upstream 
locations of the near-bottom 2 isohaline for different 
periods of the year--should be keyed to environmental goals: to 
achieving and sustaining some desired biological response level 
specified in terms of habitat protection or abundance and survival 
rates of important and diagnostic estuarine and wetland species.

Recommendations

    Goals should be expressed in terms of desired conditions for some 
future time. Progress toward those goals should be monitored and 
reported widely. Environmental goals for the estuary will be most 
effective if they are expressed in terms of restoring conditions to 
those that existed at specific historical times such as those 
summarized in Exhibit B.

(11) Conclusion

    At prevailing patterns of the position of the near-bottom 
2 isohaline, the biological resources of the low salinity 
portion of the estuary, including the Delta, have been seriously 
depleted. Data from the Interagency Ecological Studies Program and the 
University of California at Davis indicate clearly that species at 
every trophic level are now at, or near, record low levels in the Delta 
and in Suisun Bay. This is not surprising considering the recent 
drought, the introduction of exotic species, and the increased 
diversion of water.
    Analyses of the data indicate that the abundance or survival of a 
number of important species at a variety of life history states and 
from a variety of trophic levels is related to the position of the 
near-bottom 2 isohaline. Of the organisms whose response to 
salinity has been analyzed, the farther downstream the 2 
isohaline is, the higher their abundance or survival.
    Almost all of the components of the estuarine community analyzed 
during the workshops (e.g., organisms, habitats, and processes) show a 
strong, coherent, and negative monotonic response to increased 
penetration (upstream movement) of the near-bottom 2 
isohaline. There is no well-defined break point that can be reliably 
identified statistically in the composite relationship between the 
abundance or survival of these components and the position of the 
2 isohaline. In other words, the biological benefits of 
downstream displacement of the 2 continue to increase over 
the range of positions of the 2 near-bottom isohaline 
reflected in the historical data set.
    If one selects a certain level of restoration and biological 
response as a goal, then one can develop statistical relationships to 
prescribe the appropriate range of the position of the near-bottom 
2 isohaline and the amounts of water necessary to achieve 
these salinity distributions during different periods of the year. 
While such action will not guarantee achieving a desired level of 
resource recovery or protection, it would increase the probability of 
attaining these goals.

Recommendations

    A range of environmental/ecosystem restoration goals should be 
selected, and analyses should be made, to determine the distribution of 
the 2 near-bottom isohaline throughout the year consistent 
with those goals. Historical flow and salinity data should be examined 
to determine how frequently these conditions would have been met before 
construction of the Central Valley Project; the State Water Project; a 
variety of city, county, and regional projects that divert water; and 
before the large-scale reclamation of historical tidal marshlands. The 
results of these analyses would provide a valuable context within which 
to evaluate the amounts of water needs to achieve a range of ecological 
goals.

Appendix II to the Preamble--Determination of Historical Conditions

    Appendix II summarizes the methodology used in developing the 
historical conditions data presented in Table 1, above.

1. Calculating Delta Outflow Over Historical Period

    Net Delta outflow at Chipps Island is estimated by performing a 
water balance at the boundary of the Delta. The water balance involves 
adding the total Delta inflow and Delta precipitation runoff, then 
subtracting Delta channel depletions and exports. See Equation 1, 
below. DWR has estimated net Delta outflow for water years 1956-present 
with their flow accounting model, DAYFLOW. A similar model, using a 
smaller number of measured flows, was used to estimate Delta outflow 
from 1929-1962. In the years of overlap the two models yield very 
similar results.

Equation 1: Delta outflow = river inflows + precipitation - channel 
depletions--exports

    The four components used to calculate net Delta outflow are based 
on a variety of measurements. Most of the river inflows are gaged or 
directly measured at some point before they enter the Delta. Local 
precipitation is derived by multiplying the surface area of the Delta 
by the rainfall recorded at Stockton. Local precipitation is usually a 
trivial amount of flow but within-Delta uses (called channel 
depletions) can be substantial. Prior to construction of Shasta Dam and 
its regulation of Sacramento River flow, net Delta outflow was often 
negative during summer months because channel depletions exceeded Delta 
outflow. The level of channel depletions in DAYFLOW are based on 
average monthly crop demands for the acreage of each crop grown on 
Delta islands. Exports are directly measured at the point of diversion.
    Because of the arithmetic nature of these estimates of Delta 
outflow, the estimated flows cannot reflect the impacts of such factors 
as the spring/neap tidal cycles, wind, etc. that would affect the 
actual mean daily flow velocities in the western Delta.

2. Calculation of Historical Occurrence of 2 ppt Isohaline Position

    The daily estimates of net Delta outflow from October 1, 1939 to 
September 30, 1975 were used to calculate the frequency with which the 
2 ppt isohaline was downstream of each of the specified positions in 
each year. Isohaline position is a function of net Delta outflow on a 
particular day and the isohaline position on the previous day, as 
specified in Eq. 2. (Kimmerer and Monismith 1993).
Equation 2: Mean daily position of 2 ppt near-bottom isohaline (X2) on 
day t: X2(t) = 10.16 + (0.945 times X2(t-1)) - (1.487 times 
log10(Delta outflow))

3. Adjustment for Water Year Type

    The proposed criteria were developed to reflect the average 
position of the 2 ppt isohaline in different water year types, 
according to the classification adopted by the State Board (SWRCB 
1991). First, for each year from 1940 to 1975, the number of days on 
which the 2 ppt level was attained at each target location was 
tabulated. These totals were then averaged across each water year type. 
Because no critical years were available for comparison during this 
historical period, the average position of the 2 ppt isohaline in 
critical years was extrapolated from the other year types. The 
extrapolation was performed by fitting a curvilinear model to the 
averages for the other year types. These extrapolations are shown in 
Figures 1 and 2, above. The results of average number of days for each 
year type, along with the extrapolated values for critical years, are 
presented in Table 1, above.

4. Sensitivity to Starting Assumptions

    No estimate of the location of the 2 ppt isohaline on October 1, 
1939 was available, so the starting position in October 1939 was 
assumed to be 75 km. However, sensitivity analysis showed that the 
calculated isohaline position on February 1 was largely independent of 
the assumed isohaline position on the preceding October 1. This 
sensitivity analysis was performed as follows: for each of the ten 
years from 1940 to 1949, the February 1 isohaline position was 
calculated under two assumptions: (1) that the October 1 starting 
position was at the Golden Gate (km 0), and (2) that the October 1 
starting position was 100 km upstream of the Golden Gate. The 
historical delta outflow patterns and volumes differed greatly among 
these years and the calculated February 1 isohaline positions ranged 
from 49 km above the Golden Gate after wet winters to as much as 72 km 
above the Golden Gate during dry winters. However, by February 1 the 
difference in calculated positions based on the two different starting 
positions varied by no more than 0.1 km in any year.

Appendix III to the Preamble

    Appendix III describes the models used to create and measure the 
salmon smolt survival indices for the Sacramento and San Joaquin 
Rivers. These indices and the underlying models represent the state-of-
the-art analyses of the factors critical to maintaining habitat 
conditions necessary to protect cold water fish migration. 
Nevertheless, as further scientific work is completed and the new data 
is analyzed in the models, EPA anticipates that the models and indices 
will be further refined. EPA intends that these refinements be 
incorporated into the State's criteria during the triennial review 
process.

Derivation of the Sacramento River Index

    The smolt survival index for fall-run outmigrating smolts in the 
Sacramento River Delta has been developed by the US Fish and Wildlife 
Service, using coded-wire tagged hatchery-raised smolts released at 
various locations and under different conditions within the Bay/Delta, 
and recovered by trawl downstream. The methods are described in USFWS, 
1987. Since estimates of total tagged fish in the river cross-section 
(based on trawl mouth size and time fished) yielded a maximum survival 
index of nearly 1.8, and the frequency distribution plot of survival 
indices indicated an approximately normal distribution with a median 
near 1.0, the indices were divided by 1.8 to provide biologically 
meaningful survival rates.
    In order to estimate the benefits of various measures to achieve 
these indices, a multiple regression smolt survival model was developed 
for the Sacramento River portion of the Delta. The model, based on 
tagged smolt releases between 1978 and 1989, is described in Kjelson et 
al, 1989; a more recent verification and analysis is described in 
USFWS, 1992a and 1992b. The Sacramento River portion of the Delta was 
divided into three reaches for survival analysis: (1) The Sacramento 
River from Sacramento to Walnut Grove, where the Cross-Delta Channel 
and Georgiana Slough divert water from the main-stem Sacramento River 
into the central Delta; (2) Walnut Grove to Chipps Island (at the 
confluence of the Delta river systems) via the central Delta; and (3) 
Walnut Grove to Chipps Island via the Sacramento River system. Survival 
indices were converted to mortalities by subtracting from 1.0, and were 
correlated with ecologically meaningful factors for each reach. 
Multiple regression analysis was then used to develop equations for 
each reach which included the significant (p<.05) factors affecting 
mortality. The equations used to calculate mortality for each reach (as 
identified above) are:

M1 = -2.45925 + (0.0420748 * Avg Water Temp,  deg.F, at Freeport, 
CA), r2 = .39
M2 = -0.5916024 + (0.017968 * Avg Water Temp,  deg.F, at Freeport, 
CA) + (0.0000434 * SWP + CVP Exports), r2 = .69
M3 = -1.613493 + (0.0319584 * Avg Water Temp,  deg.F, at Freeport, 
CA), r2 = .32

    Using these equations, USFWS calculated total mortality for the 
Sacramento River Delta using an adaptation of an approach developed by 
Ricker (1975) describing the combined effect of two independent sources 
of mortality occurring sequentially over two distinct time periods:

MT = M1 + M2*P1 + M3*P2 - 
M1*M2*P1 - M1*M3*P2

where P1 = proportion of Sacramento River flow diverted into the 
central Delta at Walnut Grove through the Cross-Delta Channel and 
Georgiana Slough, and P2 = proportion of Sacramento River flow 
remaining in the Sacramento River. If, as happens when temperatures are 
low, the term ``M1'' is negative, it will be reset to zero before 
the computation above is made. Total survival is then calculated as:

ST = (1-MT)

    The USFWS is also estimating survival from recovery of tagged fish 
in the ocean salmon fishery. The results correlate with the 
(unadjusted) trawl recovery survival indices (p<0.01; r=0.89; USFWS 
1992b), and further increase confidence in the survival indices as a 
good measure of migration success and habitat conditions.
    Sacramento River Delta survival index values reflecting historical 
habitat conditions in different types of water years (Table 2) were 
calculated by the USFWS using the 1989 version of the above models, 
together with historical data on temperatures, water exports, and the 
percentage of Sacramento River flows diverted at Walnut Grove, as 
described in USFWS 1992a. All total survival values are calculated as 
monthly averages, and assume, based on past sampling results, that 17% 
migrate through the Delta from the Sacramento River in April, 65% in 
May, and 18% in June. At low temperatures, the Sacramento River 
regression gives mortality values (m1) of less than zero, 
indicating that the regression does not give biologically meaningful 
results at these lower temperatures. The USFWS transforms these 
negative values to zeros before calculating total survival.

Derivation of San Joaquin River Index

    The smolt survival indices for the San Joaquin River Delta were 
developed from coded-wire tagged smolt study results (USFWS 1992b). The 
CWT experiments were specifically designed to evaluate the benefit of 
constructing a barrier at the head of the Old River Channel to keep 
smolts in the main channel of the San Joaquin River. Smolts diverted 
into the Old River Channel are on a direct path to the State and 
Federal pumping plants, and are also likely subject to high 
temperatures and increased predation. The smolt survival relationship 
for smolts kept in the San Joaquin River is:

y = 0.191271+.000067x
Where y = smolt survival and x = San Joaquin flow at Stockton in cfs 
(r=0.68, n=8, p<0.10).

    There was evidence from the individual CWT studies that water 
exports had a substantial effect on survival for those smolts migrating 
down the San Joaquin to Suisun Bay. For instance, separate releases in 
1989 under high export conditions and low export conditions indicate 
approximately double the survival under low export conditions. Although 
adding exports to the regression equation did not improve it, probably 
because there are not enough experimental releases under enough variety 
of conditions to provide a significant relationship, the USFWS 
developed an additional equation to model this factor, and used both 
this equation and the above flow equation to estimate smolt survival 
indices for the San Joaquin River. A discussion of the methodology is 
provided in USFWS 1992a and 1992b. This additional relationship is:

y = (.341271-0.00025x1+0.00067x2)/1.8
Where x1 = CVP+SWP exports in cfs and x2 = flow at 
Stockton in cfs.

    Past adult escapement data was used to estimate smolt survival for 
historical conditions because there is still not enough CWT information 
under a broad enough variety of flow and export conditions to rely 
solely on CWT study results. Escapement values on the Y axis were 
replaced with survival values from 0 to 1.0. This assumes that adult 
production is an indicator of smolt survival. This assumption is 
generally valid, because less of the overall natural mortality occurs 
after the smolts enter the ocean. The relationship is as follows:

y = (4.90106+.000286x1-.000774x2)/12
where y = smolt survival, x1 = mean daily flow at Vernalis from 
March 15 to June 15, and x2 = mean daily CVP+SWP exports from 
March 15 to June 15.

    The USFWS used this relationship to estimate historical smolt 
survival indices for various periods of time (see Table 2). Further 
support for the importance of flows to salmon smolt survival comes from 
CWT study results showing a significant relationship between flow at 
Stockton and survival through the lower San Joaquin River (USFWS 
1992a).
    40 CFR part 131 is proposed to be amended as follows:

PART 131--[AMENDED]

    1. The authority citation for part 131 continues to read as 
follows:

    Authority: 33 U.S.C. 1251 et seq.

    2. Section 131.37 is proposed to be added to read as follows:


Sec. 131.37  California.

    (a) Additional Criteria. The following criteria are applicable to 
waters specified in the Water Quality Control Plan for Salinity for the 
San Francisco Bay/Sacramento-San Joaquin Delta Estuary, adopted by the 
California State Water Resources Control Board in State Board 
Resolution No. 91-34 on May 1, 1991 which is available from the Water 
Resources Control Board, State of California, PO Box 100, Sacramento, 
CA 95812:
    (1) Suisun Bay Salinity Criteria. (i) General rule. Salinity 
(measured 1 meter above bottom) shall not exceed 2 ppt (measured on a 
14-day moving average) at the stations listed in Table 1 for at least 
the number of days listed in Table 1, during the months of February 
through June. 

       Table 1. Two Parts Per Thousand (2 ppt) Salinity Criteria        
------------------------------------------------------------------------
                        Roe Island [km   Chipps Island    Confluence [km
   Water year type           64]            [km 74]            81]      
------------------------------------------------------------------------
Wet..................  133 days.......  148 days.......  150 days.      
Above normal.........  105 days.......  144 days.......  150 days.      
Below normal.........  78 days........  119 days.......  150 days.      
Dry..................  33 days........  116 days.......  150 days.      
Critically dry.......  0 days.........  90 days........  150 days.      
------------------------------------------------------------------------


    The Roe Island measurements shall be made at the salinity measuring 
station maintained by the U.S. Bureau of Reclamation at Port Chicago 
(km 64). The Chipps Island measurements shall be taken at the Mallard 
Slough Monitoring Site, Station D-10 (RKI RSAC-075) maintained by the 
California Department of Water Resources. The Confluence measurements 
shall be taken at the Collinsville Continuous Monitoring Station C-2 
(RKI RSAC-081) maintained by the California Department of Water 
Resources. Water year types shall be determined by reference to the 
Sacramento Basin Water Year Type classifications, defined in paragraph 
(c)(1)(i) of this section.
    (ii) Exception. The 2 ppt salinity criteria need not be met at the 
Roe Island station unless and until the 2 ppt salinity isohaline occurs 
at the Roe Island station due to uncontrolled hydrologic conditions. 
After such occurrence, the 2 ppt salinity criteria (measured on a 14-
day moving average) must be attained at the Roe Island station for the 
lesser of the number of days indicated in Table 1 or the number of days 
remaining in the period February 1 through June 30 after such 
occurrence. (2) Salmon Smolt Survival Criteria.--(i) General rule. 
Salmon smolt survival index values shall attain at least the values 
indicated in Table 2. 

                 Table 2. Salmon Smolt Survival Criteria                
------------------------------------------------------------------------
           Sacramento River                     San Joaquin River       
------------------------------------------------------------------------
     Water year type      Index value     Water year type    Index value
------------------------------------------------------------------------
Wet.....................  .45           Wet...............  .46         
Above normal............  .38           Above normal......  .30         
Below normal............  .36           Below normal......  .26         
Dry.....................  .32           Dry...............  .23         
Critical................  .29           Critical..........  .20         
------------------------------------------------------------------------


    (ii) Computing salmon smolt survival index values for Sacramento 
River. Index values on the Sacramento River shall be computed according 
to the following formula:

-SRSI = 1 - (-2.45925+.0420748T)
    +(-0.5916024+.017968T+.0000434E) (P1)
    +(-1.613493+.0420748T) (P2)
    -(-2.45925+.0420748T)*
    (-.5916024+.017968T+.0000434E) * P1
    -(-2.45925+.0420748T) * (-1.613493+.0420748T) * P2

where

SRSI = Sacramento River Salmon Index value
    T = Average Water Temperature in Fahrenheit at Freeport
    E = Average State Water Project plus Central Valley Project 
Exports in cubic feet/second (cfs) (from DAYFLOW)
    P1 = proportion water diverted into Delta Cross-Channel at 
Walnut Grove
    P2 = proportion water remaining in Sacramento River at 
Walnut Grove
    The index shall be computed at least monthly, weighted by the 
proportion migrating during each month (or shorter time period) and 
summed to estimate survival for the water year. Total survival for the 
entire fall-run migration period shall either use monitoring 
information collected during each water year's outmigration to 
determine the specific pattern of migration for the water year, or 
shall assume monthly migration to be 17% in April, 65% in May, and 18% 
in June. For purposes of this computation, mortality for the Sacramento 
River Reach between Sacramento and Walnut Grove (which is reflected in 
the computation above by the term ``(-2.45925+.0420748T)'') shall be 
reset to zero before the index is calculated if this term is negative, 
as happens at low temperatures.
    (iii) Computing salmon smolt survival index values for San Joaquin 
River. Index values on the San Joaquin River shall be computed 
according to the following formula:

SJSI = (0.341271-0.000025E+0.000067F)/1.8

where

SJSI = San Joaquin River Salmon Index value
    E = Average Central Valley Project plus State Water Project 
exports measured in cfs
    F = Mean daily flow in cfs in San Joaquin River at Stockton, 
calculated as Old River flow subtracted from San Joaquin River flow 
at Mossdale. Old River flow is calculated from ratio of Brandt 
Bridge flow to exports.

The index shall be computed at least monthly, weighted by the 
proportion migrating during each month (or shorter time period) and 
summed to estimate survival for the water year. Total survival for the 
entire fall-run migration period shall either use monitoring 
information collected during each water year's outmigration to 
determine the specific pattern of migration for the water year, or 
shall assume monthly migration to be 45% in April and 55% in May.
    (b) Revised Criteria. The following criteria are applicable to 
state waters specified in Table 1-1, at Section (C)(3) (``Striped 
Bass--Salinity : 3. Prisoners Point--Spawning'') of the Water Quality 
Control Plan for Salinity for the San Francisco Bay--Sacramento/San 
Joaquin Delta Estuary, adopted by the California State Water Resources 
Control Board in State Board Resolution No. 91-34 on May 1, 1991:

--------------------------------------------------------------------------------------------------------------------------------------------------------
                             Sampling site                                                                                                              
        Location            Nos. (I-A/RKI)        Parameter             Description            Index type        Year type           Dates        Values
--------------------------------------------------------------------------------------------------------------------------------------------------------
San Joaquin River at       D15/RSAN018, C4/   Electrical          14-day running average    Not Applicable    Wet, Above        April 1 to May      0.44
 Jersey Point, San          RSAN032, D29/      Conductivity (EC)   of mean daily for the                       normal, and       31                     
 Andreas Landing,           RSAN038, P8/                           period not more than                        below normal                             
 Prisoners Point, Buckley   RSAN056, -/                            value shown, in mmhos.                      years                                    
 Cove, Rough and Ready      RSAN062, C6/                                                                                                                
 Island, Brandt Bridge,     RSAN073, C7/                                                                                                                
 Mossdale, and Vernalis.    RSAN087, C10/                                                                                                               
                            RSAN112                                                                                                                     
San Joaquin River at       D15/RSAN018, C4/   Electrical          14-day running average    Not Applicable    Dry and critical  April 1 to May     0.44 
 Jersey Point, San          RSAN032, D29/      Conductivity (EC)   of mean daily for the                       dry years         31                     
 Andreas Landing and        RSAN038                                period not more than                                                                 
 Prisoners Point.                                                  value shown, in mmhos.                                                               
--------------------------------------------------------------------------------------------------------------------------------------------------------


    (c) Definitions. Terms used in paragraphs (a) and (b) of this 
section, shall be defined as follows:
    (1) Water year type.
    (i) Sacramento Basin Water Year Type. Water year types in the 
Sacramento River basin are computed as follows:
    (A) The Sacramento Basin Index is computed according to the 
following formula:

ISAC=0.4X+0.3Y+0.3Z
where ISAC=Sacramento Basin Index
    X = April through July Four River Unimpaired Flow in Million 
Acre Feet (MAF)
    Y = October through March Four River Unimpaired Flow in MAF
    Z = Previous Year's Sacramento Basin Index in MAF, not to exceed 
10 maf

    (B) Measuring Four River Unimpaired Flow. The Four River Unimpaired 
Flow for a current water year (October 1 to September 30) is a forecast 
of the sum of the following locations: Sacramento River above Bend 
Bridge, near Red Bluff; total inflow to Oroville Reservoir; Yuba River 
at Smartville; American River, total inflow to Folsom Reservoir. The 
flow determinations are made and are published by the California 
Department of Water Resources in Bulletin 120 which is available from 
the California Department of Water Resources, 3251 S Street, 
Sacramento, CA 95816. Preliminary determinations of year classification 
shall be made in February, March, and April with final determination in 
May. These preliminary determinations shall be based on hydrological 
conditions to date plus forecasts of future runoff assuming normal 
precipitation for the remainder of the water year.
    (C) Sacramento River Basin Water Year Type shall be categorized 
according to the following table:

------------------------------------------------------------------------
 Sacramento basin water year type        Sacramento basin index value   
------------------------------------------------------------------------
Wet (W)............................   9.2 MAF.               
Above normal (AN)..................  < 9.2 MAF, > 7.8 MAF.              
Below normal (BN)..................   7.8 MAF, > 6.5 MAF.    
Dry (D)............................   6.5 MAF, > 5.4 MAF.    
Critical (C).......................   5.4 MAF.               
------------------------------------------------------------------------


    (ii) San Joaquin Basin Water Year Type.
    Water year types in the San Joaquin River Basin are computed as 
follows:
    (A) The San Joaquin Valley Index is computed according to the 
following formula:

ISJ=0.6X+0.2Y and 0.2Z
where ISJ=San Joaquin Valley Index
    X = Current year's April-July San Joaquin Valley unimpaired 
runoff
    Y = Current year's October-March San Joaquin Valley unimpaired 
runoff
    Z = Previous year's index in MAF, not to exceed 0.9 MAF

    (B) Measuring San Joaquin Valley unimpaired runoff. San Joaquin 
Valley unimpaired runoff for the current water year from the preceding 
year's October 1 to September 30 of the current calendar year) is a 
forecast of the sum of the following locations: Stanislaus River, total 
flow to New Melones Reservoir; Tuolumne River, total inflow to Don 
Pedro Reservoir; Merced River, total flow to Exchequer Reservoir; San 
Joaquin River, total inflow to Millerton Lake. Preliminary 
determinations of year classification shall be made in February, March 
and April with final determination in May. These preliminary 
determinations shall be based on hydrologic conditions to date plus 
forecasts of future runoff assuming normal precipitation for the 
remainder of the water year.
    (C) San Joaquin Valley Water Year Type shall be categorized 
according to the following table: 

------------------------------------------------------------------------
San Joaquin valley water year type      San Joaquin valley index value  
------------------------------------------------------------------------
 Wet (W)...........................   3.8 MAF.               
Above normal (AN)..................  < 3.8 MAF, > 3.1 MAF.              
Below normal (BN)..................   3.1 MAF, > 2.5 MAF.    
Dry (D)............................   2.5 MAF, > 2.1 MAF.    
Critical (C).......................   2.1 MAF.               
------------------------------------------------------------------------


    (2) Water year. A water year is the twelve calendar months 
beginning October 1.

[FR Doc. 94-120 Filed 1-5-94; 8:45 am]
BILLING CODE 6560-50-P