Requires the Federal agencies to: (1) coordinate their activities with specified California agencies; (2) cooperate with local and tribal governments and the public through a federally chartered advisory committee or other means; and (3) implement the Program using the best available scientific information and scientific review.

Directs the Secretary: (1) to report monthly on the Authority's progress in achieving the water supply targets, environmental water account requirements, and water quality targets described in the Record and on any pending actions that may affect the Authority's ability to achieve those targets and requirements; (2) to report annually on Program implementation, expenditures, and accomplishments; (3) to certify in such annual report whether the Program is progressing in a balanced manner in advancing Program components (requires the Authority to prepare a revised implementation schedule to ensure balanced progress if balance is not certified); (4) to submit annual financial reports containing a detailed accounting of all Federal and State funds received and obligated under the Program and all projects to be carried out in the upcoming year; (5) prior to December 2004, to report to Congress on the Program's accomplishments, the specific steps remaining to be undertaken, the specific funding levels and sources to accomplish such steps, and recommendations necessary to accomplish Program goals and objectives.

Requires: (1) the President's budget to include requests for an appropriate funding level for each Federal agency to carry out its Program responsibilities; and (2) the Office of Management and Budget to submit an interagency budget crosscut report displaying the budget proposed for each such agency for the Program.

Prohibits the Federal share of the total cost of implementing Stage 1 from exceeding 33.3 percent.