Great Lakes Collaboration Implementation Act

Great Lakes Collaboration Implementation Act - Amends the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 to: (1) require certain vessels operating in U.S. waters to have invasive species management plans; (2) direct the Secretary of Homeland Security to establish vessel performance requirements, including provisions for ballast water exchange, treatment, and discharge, and civil and criminal penalties for violations; (3) require federal agencies to restrict the importation of live aquatic organisms of species not in trade without screening and approval; and (4) declare importation of such species to be unlawful and prescribe civil and criminal penalties for violations.

Directs the Secretary of the Army to: (1) upgrade and make permanent the Chicago sanitary and ship canal dispersal barrier in Chicago, Illinois; (2) construct Barrier II; and (3) operate and maintain Barriers I and II.

Renames the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 as the Nonindigenous Aquatic Invasive Species Prevention and Control Act of 1990.

National Invasive Species Council Act - 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 (NISC) 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. Requires NISC to develop a National Invasive Species Management Plan and to establish an Invasive Species Advisory Committee.

Reauthorizes and modifies the Great Lakes Fish and Wildlife Restoration Act of 1990.

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) replace each reference to "navigable waters of the United States" with a reference to "waters of the United States"; (4) require the Great Lakes National Program Office to provide grants to reduce the quantity of mercury in the Great Lakes; and (5) require the President include a joint Great Lakes research plan in the annual budget submitted to Congress.

Authorizes funding for the Great Lakes Environmental Research Laboratory. Requires the National Oceanic and Atmospheric Administration (NOAA) to provide grants for Great Lakes research and monitoring activities.

Requires: (1) the President, acting through the National Ocean Research Leadership Council, to establish a system that detects and predicts changes in the ocean, coastal, and Great Lakes environment that impact certain U.S. systems; and (2) the 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 meetings and make recommendations and reports on Great Lakes restoration goals and progress; and (3) the Great Lakes Regional Collaboration to develop 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.