Extends from July 31, 2010, to December 18, 2013, the termination of the prohibition against the Administrator of the Environmental Protection Agency (EPA), or a state with an approved National Pollutant Discharge Elimination System (NPDES) permit program under the Federal Water Pollution Control Act (commonly known as the Clean Water Act) requiring an NPDES permit for a vessel that is less than 79 feet in length or a fishing vessel for any discharge: (1) of effluent from properly functioning marine engines; (2) of laundry, shower, and galley sink wastes; or (3) that is incidental to the normal operation of the vessel.

Title II: Clean Estuaries - Clean Estuaries Act of 2010 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to reauthorize the National Estuary Program.

Revises the purpose of management conferences convened with respect to estuaries to expand requirements governing a comprehensive conservation and management plan by requiring such a plan to: (1) identify the estuary and its associated upstream waters to be addressed by the plan; (2) consider sustainable commercial activities in the estuary; (3) address the impacts of climate change on the estuary; (4) increase public education and awareness with respect to the ecological health and water quality conditions of the estuary and to ocean, estuarine, land, and atmospheric connections and interactions; (5) identify and assess impairments coming from outside of the area addressed by the plan and the sources of those impairments; (6) include performance measures and goals to track implementation of the plan; (7) include a coordinated monitoring strategy for government and other entities; (8) monitor (and make results available to the public regarding) water quality conditions in the estuary and its associated upstream waters, habitat conditions that relate to the ecological health and water quality conditions of the estuary, and the effectiveness of actions taken pursuant to the plan; and (9) provide information and educational activities on the estuary's ecological health and water quality conditions.

Requires a management conference's membership to include, among other entities, not-for-profit organizations.

Requires a management conference, in updating or developing a new plan, to make use of collaborative processes to: (1) ensure equitable inclusion of affected interests and the accessibility of relevant information to members; (2) engage with members of the conference through the use of consensus-based decision rules and assistance from impartial facilitators; (3) promote accountability and transparency by ensuring members are informed of conference purposes and objectives and evaluation results in a timely manner; (4) identify roles and responsibilities of members in conference proceedings and plan implementation; and (5) seek resolution of conflicts or disputes.

Requires the Administrator of the Environmental Protection Agency (EPA) to: (1) evaluate, every four years, the implementation of each comprehensive conservation and management plan developed under the Program to determine the degree to which the goals of the plan have been met; (2) submit the results of the evaluation to the appropriate management conference for review and comment; and (3) report on the results of the evaluation and make such report available to the public in the Federal Register and on the Internet. Requires management conferences to update plans 18 months after they are evaluated.

Authorizes the Administrator to consider a management conference to be in probationary status if the conference has not received approval for an updated plan within three years of the date of the evaluation's publication. Requires the Administrator to: (1) reduce a grant for the implementation of a plan developed by a management conference with probationary status; and (2) terminate a management conference and cease funding for the implementation of the plan if the conference has been in probationary status for two consecutive years.

Requires, after the Administrator's approval of a plan for an estuary, any federal action or activity affecting such estuary to be conducted in a manner consistent with such plan. Requires the Secretary of the Army, the Administrator of the National Oceanic and Atmospheric Administration (NOAA), the Director of the United States Fish and Wildlife Service, the Chief of the Natural Resources Conservation Service, and the heads of other appropriate federal agencies to: (1) cooperate and coordinate activities, including monitoring activities, related to the implementation of such plans; and (2) collaborate on the development of tools and methodologies for monitoring the ecological health and water quality conditions of estuaries covered by a management conference. Makes EPA the lead coordinating agency for implementing plans.

Requires an agency head, in making annual budget requests, to consider the agency's responsibilities under the Program.

Repeals provisions authorizing the Administrator to give grants to individuals for the development and implementation of plans.

Authorizes appropriations for FY2011-FY2016 for management conferences, grants, and monitoring the administration of plans.

Requires the Administrator to include measures to track the introduction and establishment of non-native species within the trend assessment program that monitors variations in environmental parameters which may affect estuarine zones.

Requires the Administrator, every four years, to: (1) evaluate the effectiveness of the Program in, and identify best practices for, improving water quality, natural resources, and sustainable uses of estuaries covered by conferences; (2) identify and develop a plan for limiting redundant requirements for reporting by grant recipients; and (3) report on such evaluation to management conferences convened and the public.

Repeals provisions directing the Administrator to give priority to specified areas in the convening of conferences. Revises the definition of: (1) "estuary" to include near coastal waters and other bodies of water within the Great Lakes similar in form and function to waters otherwise described in such definition; and (2) "estuarine zones" to include such waters and transitional areas, associated aquatic ecosystems, and those portions of tributaries.