Great Lakes Collaboration Implementation Act of 2006

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 (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 of such species. Requires NISC to develop a National Invasive Species Management Plan and to establish an Invasive Species Advisory Committee.

Great Lakes Fish and Wildlife Restoration Act of 2006 - 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) require the Great Lakes National Program Office to provide grants to reduce the quantity of mercury in the Great Lakes; and (4) require the President include a joint Great Lakes research plan in the annual budget submitted to Congress.

Requires: (1) the National Oceanic and Atmospheric Administration (NOAA) to provide grants for Great Lakes research and monitoring activities; (2) the President to establish a system that detects and predicts changes in the ocean, coastal, and Great Lakes environment that impact certain U.S. systems; and (3) 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 observing 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.