Puget Sound Recovery Act of 2009

Puget Sound Recovery Act of 2009 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to direct the Administrator of the Environmental Protection Agency (EPA) to: (1) establish a Puget Sound Program Office, to be co-located with the Puget Sound Partnership in Washington; and (2) appoint a Director of the Office.

Requires the Administrator, acting through the Director, to: (1) assist and support the implementation of the Puget Sound Action Agenda; (2) provide funding and make grants for implementation of the Agenda and related projects; (3) promote methodologies and technologies that are cost-effective and consistent with the goals and objectives of the Agenda and the EPA permitting processes; (4) coordinate the major functions of the federal government relating to the implementation of the Agenda; (5) coordinate the research and planning projects authorized under this Act with federal and state agencies, tribes, universities, and the Puget Sound Partnership's Science Panel; (6) track progress toward meeting the identified goals and objectives of the Agenda; (7) coordinate projects, programs, and studies for the protection of Puget Sound, the Strait of Georgia, and the Strait of Juan de Fuca with Canadian authorities; (8) collect and make available to the public publications and information relating to the environmental quality of Puget Sound; and (9) implement projects, programs, and studies to implement the Agenda.

Requires the Administrator to establish a Puget Sound Program Advisory Council to provide advice on the implementation of the Agenda's goals and objectives.

Requires the Administrator and the Executive Director of the Puget Sound Partnership to a report, biennially, to Congress on implementation of the Agenda.

Allows the Administrator, acting through the Director, to make grants for projects, programs, and studies to implement the Agenda, including a comprehensive grant to the Partnership to manage such implementation.

Requires the President, as part of the annual budget, to submit information regarding expenditures and roles of each federal agency involved in Puget Sound protection and restoration.