Great Lakes Ecosystem Protection Act of 2010

Great Lakes Ecosystem Protection Act of 2010 - Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to expand the duties of the Great Lakes Program Office by requiring the Office to: (1) provide support for Great Lakes governance and management; and (2) coordinate with the Great Lakes Interagency Task Force.

Establishes: (1) the Great Lakes Leadership Council to establish policy, goals, and priorities with respect to Great Lakes protection and restoration, determine a process for participating in international forums, and provide annual input regarding federal budget priorities and levels for Great Lakes protection and restoration; (2) the Great Lakes Management Committee within the Council to report to and provide direction for the Council, monitor and assist implementation activities relating to Great Lakes management, and engage in problem solving regarding Great Lakes management; and (3) the Great Lakes Interagency Task Force.

Requires the Administrator of the Environmental Protection Agency (EPA) to report annually to Congress on budgets and restoration activities relating to EPA's organizational elements involved in Great Lakes activities and EPA's reasons for approving or disapproving the Council's recommendations.

Authorizes appropriations for: (1) remediation of sediment contamination in areas of concern in the Great Lakes; and (2) the Great Lakes Program.

Requires EPA, in coordination with federal partners, to implement a Great Lakes Restoration Initiative which will: (1) identify and support programs to target the most significant environmental problems in the Great Lakes ecosystem; (2) be based on the work of the Task Force and the Council's stakeholders and nongovernmental partners; and (3) represent the government's commitment to significantly advance Great Lakes protection and restoration. Prohibits funding made available to implement the Initiative from being used for water infrastructure activity that is implemented using funds made available under the clean water or drinking water state revolving fund program.

Requires federal agencies to: (1) maintain the base level of funding for their Great Lakes activities; and (2) identify new activities to support the environmental goals of the Initiative.