Great Lakes Ecosystem Protection Act of 2012 - 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 of 1978 (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 coordinating with the Great Lakes Interagency Task Force (Task Force), established by this Act.
Requires the Administrator of EPA to establish the Great Lakes Advisory Board to provide advice and recommendations to the Administrator on matters pertaining to Great Lakes restoration and protection.
Finds that the Great Lakes Restoration Initiative (Initiative), which commenced in 2010, is designed to: (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 and the Advisory Board, stakeholders, and nongovernmental partners; and (3) represent the government's commitment to significantly advancing Great Lakes protection and restoration.
Requires the Initiative to prioritize work done by non-federal partners using funding made available for the Great Lakes for priority areas for each fiscal year, such as: (1) the remediation of toxic substances and areas of concern, (2) the prevention and control of invasive species and their impacts, (3) the protection and restoration of near-shore health and the prevention and mitigation of nonpoint source pollution, and (4) habitat and wildlife protection and restoration.
Requires that: (1) Initiative funds be used to strategically implement federal projects and projects carried out in coordination with states, Indian tribes, municipalities, institutions of higher education, and other organizations; and (2) Initiative projects be carried out on multiple levels, including local, Great Lakes-wide, and Great Lakes basin-wide. 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 appropriations for the Initiative for FY2013-FY2017.
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 Agreement, the Action Plan, and the Strategy; (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 and ensure that federal policies, strategies, projects, and priorities support measurable results and are consistent with the Strategy and Action Plan; (5) exchange information regarding policies, strategies, projects, and activities of the agencies represented on the Task Force relating to the System, the Strategy, the Agreement, and the Action Plan; (6) coordinate government action associated with the System; (7) ensure coordinated federal scientific and other research associated with the System; (8) provide assistance and support to agencies represented on the Task Force in activities relating to the System; (9) establish annual priorities with respect to Great Lakes protection and restoration; and (10) review and update such Strategy and Action Plan every five years.
Requires the Administrator to submit to Congress annually a comprehensive report on the overall health of the Great Lakes, including a description of the achievements in implementing the Agreement, a list of the Initiative's accomplishments, and recommendations for streamlining work of existing advisory and coordinating committees.
Requires the Director of the Office of Management and Budget (OMB) to submit to Congress, annually, a financial report certified by each agency that has budget authority for Great Lakes restoration activities that contains: (1) an interagency budget crosscut report, (2) a detailed accounting of all funds received and obligated by all federal agencies and state agencies using federal funds for Great Lakes restoration activities during the current and previous fiscal years, (3) a budget for the proposed projects to be carried out in the subsequent fiscal year, and (4) a listing of projects to be undertaken in the subsequent fiscal year.
Authorizes appropriations for: (1) remediation of sediment contamination in areas of concern in the Great Lakes, and (2) the Great Lakes Program.