Chesapeake Clean Water and Ecosystem Restoration Act of 2009

Chesapeake Clean Water and Ecosystem Restoration Act of 2009 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to: (1) revise and expand definitions under the Chesapeake Bay Program; (2) expand the implementation and monitoring grant programs; and (3) require that at least 10% of funds for implementation grants be made available to the states of Delaware, New York, and West Virginia, and that at least 20% of such funds be made available to Chesapeake Bay States (i.e., Delaware, Maryland, New York, West Virginia, Pennsylvania, Virginia, and the District of Columbia) to provide technical assistance to agricultural producers and foresters.

Requires the Administrator of the Environmental Protection Agency (EPA) to: (1) make public by March 31 of each year a Chesapeake Bay action plan to protect and restore the Chesapeake Bay; (2) establish a Chesapeake Bay Stewardship Grants Program; (3) establish minimum criteria for watershed implementation plans; (4) establish by December 31, 2010, a Chesapeake Bay-wide TMDL (total maximum daily load for nitrogen, phosphorus, and sediment loading to the waters in the Chesapeake Bay); (5) establish by May 12, 2012, an interstate nitrogen and phosphorus trading program for the Chesapeake Bay; (6) designate the Asian oyster (species Crassostrea ariakensis) as a biological pollutant in the Chesapeake Bay; and (7) conduct a study on the impacts of the commercial harvesting of Menhaden (species Brevoortia tyrannus) on Chesapeake Bay water quality.

Requires each Chesapeake Bay State to: (1) submit to the Administrator by May 12, 2011, a watershed implementation plan to be fully implemented by May 12, 2025; and (2) institute a ban on phosphorus cleaning agents within three years after the enactment of this Act.

Authorizes the Secretary of the Interior to provide funds to the states of Delaware, Maryland, and Virginia to carry out a program to eradicate or control nutria (species Myocaster coypus) and restore marshland destroyed by nutria.

Authorizes appropriations for FY2010-FY2015 for nonpoint source management programs (reduction of water pollution from land use practices).