Great Lakes Fish and Wildlife Restoration Act of 2006 - Amends the Great Lakes Fish and Wildlife Restoration Act of 1990 to require the Director of the U.S. Fish and Wildlife Service (FWS) to implement fish and wildlife restoration proposals and regional projects if funding is available. Defines "regional projects" as authorized activities of FWS related to fish and wildlife resource protection, restoration, maintenance, and enhancement that benefit the Great Lakes basin.
Requires the Great Lakes Fish and Wildlife Restoration Proposal Review Committee to operate under the guidance of FWS (currently, under the guidance of the Council of Lake Committees of the Great Lakes Fishery Commission) and revises Committee membership requirements.
Revises the goals of FWS programs related to the Great Lakes fish and wildlife resources to include restoring and maintaining self-sustaining fish and wildlife resources.
Requires the Great Lakes Coordination Office to: (1) ensure that information acquired under such Act is made available to the public; and (2) report to the FWS Director of Region Three, Great Lakes Big Rivers.
Includes within the responsibilities of the Lower Great Lakes Fishery Resources Office and the Upper Great Lakes Fishery Resources Offices FWS operational activities related to fishery resource protection, restoration, maintenance, and enhancement in the offices' respective regions.
Requires the Director to: (1) submit annual reports to the eight Great Lakes States and Indian Tribes; and (2) conduct a comprehensive study of the status, assessment, management, and restoration needs of the fish and wildlife resources of the Great Lakes Basin. Authorizes appropriations.