Great Lakes Collaboration Implementation Act of 2009

Great Lakes Collaboration Implementation Act of 2009 - National Aquatic Invasive Species Act of 2009 - Amends the Nonindigenous Aquatic Nuisance Prevention and Control Act of 1990 to: (1) require the Aquatic Nuisance Species Task Force to conduct a priority program to manage pathways that pose the highest risk for introduction of invasive species; (2) prohibit aquatic organisms from being imported without screening and approval; (3) require the Director of the U.S. Geological Survey (USGS) and the Administrators of the National Oceanic and Atmospheric Administration (NOAA) and the Environmental Protection Agency (EPA) to implement a national system of ecological surveys to rapidly detect recently established aquatic invasive species in U.S. waters; (4) establish the Emergency Rapid Response Fund to provide financial assistance to state or federal rapid response teams implementing rapid response measures for aquatic invasive species; and (5) require the Secretary of the Interior to establish an interbasin and intrabasin monitoring program to track invasive species moving through interbasin waterways and specified major river systems and to identify waterways suitable for dispersal barrier demonstration projects.

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

Prohibits importation of a specified carp species. Directs the Assistant Secretary of the Army for Civil Works to upgrade and make permanent the sanitary and ship canal dispersal barrier in Chicago, Illinois.

Prohibits federal agencies from promoting the introduction or spread of invasive species unless the benefits outweigh the harm.

Establishes the National Invasive Species Council to: (1) lead and coordinate efforts to minimize the negative effects caused by, and to reduce the threat of further invasions of, invasive species; (2) develop a National Invasive Species Management Plan; and (3) establish an Invasive Species Advisory Committee.

Amends the Federal Water Pollution Control Act to: (1) authorize the EPA Administrator 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 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 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 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 report on Great Lakes restoration goals and progress; (3) the Great Lakes Regional Collaboration; and (4) the Great Lakes Environmental Restoration Grant Program.

Provides funding for a variety of Great Lakes programs.