Anacostia Watershed Initiative Act of 2003

Anacostia Watershed Initiative Act of 2003 - Amends the Federal Water Pollution Control Act to establish within the Environmental Protection Agency (EPA) the Anacostia Watershed Restoration Initiative.

Creates the Anacostia Watershed Council to develop, carry out, and provide assistance and recommendations with respect to the Initiative. Requires the Council to develop a ten-year comprehensive action plan for the Anacostia Watershed in Maryland and the District of Columbia.

Requires the EPA Administrator to approve the Council's action plan if it meets the requirements of this Act.

Directs the Council to submit annual reports on the Initiative to appropriate committees of Congress.

Authorizes the Administrator to provide eligible entities with financial and technical assistance to: (1) conduct research; (2) implement the approved action plan; (3) provide interdisciplinary training; (4) enhance understanding of environmental issues; and (5) develop and disseminate educational resources and opportunities. Limits Federal funds available under this Act or the Water Resources Development Act of 1992 (WRDA) for such assistance to 75 percent of total project costs.

Requires specified Federal agencies to assist the Initiative.

Amends the WRDA to authorize the Secretary of the Army to provide funding for implementation of a combined sewer overflow control plan in the District of Columbia.

Requires the Secretary, acting through the Chief of Engineers, to establish a program to provide environmental assistance to non-Federal interests in the Anacostia River Basin. Limits the Federal share of funds for such cooperation agreements to 75 percent of total project costs, except that the non-Federal share for operation and maintenance costs shall be 100 percent.