National Fish Habitat Conservation Act

Establishes Partnership approval criteria, including that a Partnership: (1) include representatives of a diverse group of public and private partners focused on conservation of aquatic habitats to achieve results across jurisdictional boundaries and public and private land, and (2) is able to address issues and priorities on a nationally significant scale.

(Sec. 6) Requires each Partnership to annually submit to the Board a list of fish habitat conservation projects recommended by the Partnership for annual funding under this Act.

Prohibits a fish habitat conservation project from being recommended by the Board unless at least 50% of the cost will be funded with non-federal funds, except that: (1) federal funds may be used for payment of 100% of the costs of such a project located on federal land or water, and (2) any funds made available to an Indian tribe under this Act may be considered non-federal funds.

(Sec. 7) Requires the Director of the U.S. Fish and Wildlife Service to establish the National Fish Habitat Conservation Partnership Office within the Service which shall: (1) provide funding for the operational needs of the Partnerships, (2) provide funding to support the detail of state and tribal fish and wildlife staff to the Office, (3) facilitate the cooperative development and approval of Partnerships, (4) assist the Secretary of the Interior, (5) facilitate efficient operations for the benefit of Partnerships and the Board, (6) facilitate the consideration of fish habitat conservation projects by the Board, (7) provide support to the Director regarding the development and implementation of the interagency operational plan, (8) coordinate technical and scientific reporting, (9) facilitate the efficient use of resources and activities of federal departments and agencies to carry out this Act, and (10) provide support to the Board for national communication and outreach efforts that promote public awareness of fish habitat conservation.

Requires the Director to develop an interagency operational plan for the National Fish Habitat Conservation Partnership Office that describes: (1) the needs of the Office, and (2) any interagency agreements between or among federal departments and agencies to address those needs.

(Sec. 8) Requires the Director to provide scientific and technical assistance to the Partnerships, participants in fish habitat conservation projects, and the Board.

(Sec. 9) Requires, to the extent consistent with the mission and authority of the applicable agency, the head of each federal agency responsible for acquiring, managing, or disposing of federal land or water to cooperate with the Assistant Administrator for Fisheries of the National Oceanic and Atmospheric Administration (NOAA) and the Director to conserve the aquatic habitats for fish and other aquatic organisms within such areas.

(Sec. 10) Requires the Secretary to provide a notice to, and coordinate with, the appropriate state agency or tribal agency within the boundaries of which an activity is planned to be carried out pursuant to this Act.

(Sec. 11) Sets forth accountability and reporting requirements.

(Sec. 13) Sets forth provisions stating the effect of this Act on water rights, states, and Indian tribes.

Prohibits this Act from permitting the use of funds made available to carry out this Act for fish and wildlife mitigation purposes under: (1) the Federal Water Pollution Control Act (commonly known as the Clean Water Act), (2) the Fish and Wildlife Coordination Act, (3) the Water Resources Development Act of 1986, or (4) any other federal law or court settlement.

(Sec. 15) Authorizes appropriations for FY2012-FY2016.

Sets forth provisions permitting agreements and grants, and the acceptance of donations, for purposes of carrying out this Act.