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 include as a purpose of such Act to achieve the goals established in the Great Lakes Restoration Initiative Action Plan (Action Plan), the Great Lakes Regional Collaboration Strategy (Strategy), and the Great Lakes Water Quality Agreement (Agreement) through: (1) improved organization and definition of mission on the part of the Environmental Protection Agency (EPA); (2) the funding of grants, contracts, and interagency agreements for protection, restoration, and pollution control in the Great Lakes area; and (3) improved accountability.

Expands the duties of the Great Lakes Program Office to include: (1) providing support for Great Lakes governance and management; and (2) coordinating with the Great Lakes Interagency Task Force (Task Force).

Establishes the Great Lakes Leadership Council (Council) to: (1) review, every five years, such Strategy and revise it if necessary; (2) establish annual priorities with respect to Great Lakes protection and restoration; (3) report to Congress, the President, and the public on the progress made in Great Lakes protection and restoration; (4) make recommendations to the Administrator of EPA and the Secretary of State regarding a process for participation in international forums, such as the Agreement, and regarding whether any existing advisory committees are duplicative and should be replaced; and (5) make recommendations to Congress and the President for streamlining the work of existing advisory and coordinating committees. Requires the Council's nonfederal members to provide input annually to the Council and the Task Force on federal budget priorities and funding levels for Great Lakes protection and restoration.

Requires the Council to establish the Great Lakes Advisory Committee to report to and provide advice to the Council on monitoring implementation activities relating to Great Lakes management and other relevant Great Lakes issues.

Requires the EPA to commence implementation of a new Great Lakes Restoration Initiative (Initiative), which shall: (1) identify programs and projects that are strategically selected to target the most significant environmental problems in the Great Lakes ecosystem; (2) be based on the work of the Task Force, the Council, stakeholders, and nongovernmental partners; and (3) represent the government's commitment to significantly advancing Great Lakes protection and restoration. Requires that the Initiative give priority to work done by nonfederal partners using funding made available for the Great Lakes for priority areas for each fiscal year. Authorizes the Administrator: (1) to transfer funding to agencies to support such Initiative and the Agreement; and (2) make grants for carrying out planning, research, monitoring, outreach, training, studies, surveys, investigations, experiments, demonstration projects, and implementation relating to the Initiative's activities. Requires the Initiative's projects to be carried out on multiple levels, including local, Great Lake-wide, and Great Lakes basin-wide levels. Prohibits funding made available to implement the Initiative from being used for any water infrastructure activity (other than a green infrastructure project that improves habitat and other ecosystem functions in the Great Lakes) 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. Authorizes funding for the Initiative.

Establishes the Task Force to: (1) collaborate with Canada, provinces of Canada, and binational bodies involved in the Great Lakes region regarding policies, strategies, projects, and priorities for the Great Lakes System; (2) coordinate the development of federal policies, strategies, projects, and priorities for addressing the restoration and protection of the System consistent with the Strategy, the Action Plan, the Agreement, and federal implementation of the Council's recommendations; (3) assist in the appropriate management of the System; (4) develop goals for the System that focus on outcomes such as cleaner water, sustainable fisheries, and biodiversity; (5) ensure that federal policies, strategies, projects, and priorities support measurable results and are consistent with the Strategy and Action Plan; (6) exchange information regarding policies, strategies, projects, and activities of the agencies represented on the Task Force relating to the System, the Strategy, and the Action Plan; (7) coordinate government action and research associated with the System; (8) ensure coordinated federal scientific and other research associated with the System; and (9) provide assistance and support to agencies represented on the Task Force in activities relating to the System.

Requires the Administrator to report annually to Congress on the overall health of the Great Lakes, the Initiative's accomplishments, recommendations for streamlining work of existing advisory and coordinating committees, 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.