Great Lakes Collaboration Implementation Act of 2007

Amends the federal criminal code to prohibit importation of specified carp species into the United States. Directs the Assistant Secretary of the Army for Civil Works to: (1) upgrade and make permanent the Chicago sanitary and ship canal dispersal barrier in Chicago, Illinois; and (2) construct dispersal barriers as necessary.

Prohibits federal agencies from authorizing, funding, or carrying out any action that would promote the introduction or spread of invasive species unless the benefits of the action outweigh the harm.

Establishes the National Invasive Species Council as an independent entity in the executive branch to lead and coordinate efforts to minimize the negative effects caused by invasive species and to reduce the threat of further invasions of such species. Requires the Council to develop a National Invasive Species Management Plan and to establish an Invasive Species Advisory Committee.

Amends the Federal Water Pollution Control Act to: (1) authorize the Administrator of the Environmental Protection Agency (EPA) to provide funding for wastewater assistance to certain municipalities and small publicly-owned treatment works; (2) authorize states to provide additional subsidization to benefit certain municipalities or state agencies that already receive assistance from the water pollution control revolving fund or to implement certain alternative techniques; (3) require the Great Lakes National Program Office to provide grants to reduce the quantity of mercury and to identify emerging contaminants in the Great Lakes; and (4) require the President include a joint Great Lakes research plan in the annual budget submitted to Congress.

Authorizes the Director of the National Oceanic and Atmospheric Administration's (NOAA) Center for Sponsored Coastal Ocean Research to provide grants to carry out activities in accordance with the joint research and monitoring plan developed by the Great Lakes National Program Office and the Great Lakes Research Office.

Requires: (1) the President to establish a system that detects and predicts changes in the ocean, coastal, and Great Lakes environment that impact the U.S. economy or ecology; and (2) the National Ocean Research Leadership Council to establish an interagency program office to be known as OceanUS to be responsible for program planning and coordination of such system.

Amends the Federal Water Pollution Control Act to require the Program Office to develop specified science-based indicators of water quality and related environmental factors in the Great Lakes.

Authorizes the Secretary to: (1) provide financial assistance for certain restoration or remediation projects; and (2) restore and remediate waterfronts and related areas.

Establishes: (1) the Great Lakes Interagency Task Force, as established by Executive Order 13340, as a task force within EPA; (2) a Great Lakes Regional Collaboration Executive Committee to hold public meetings and make recommendations and reports on Great Lakes restoration goals and progress; and (3) the Great Lakes Regional Collaboration to maintain a restoration and protection strategy for use in Great Lakes program implementation and funding decisions, to serve as a forum for addressing regional issues relating to ecosystem restoration and protection of the Great Lakes, and to establish an oversight forum to coordinate and enhance implementation of Great Lakes programs.

Provides funding for a variety of Great Lakes programs.