National Oceans Protection Act of 2005

National Oceans Protection Act of 2005 - Declares the purpose of this Act is to secure for future U.S. generations a full range of benefits of healthy marine ecosystems.

Ernest "Fritz" Hollings National Ocean Policy and Leadership Act - Specifies a national ocean policy.

Establishes in federal law (as it already exists under Reorganization Plan No. 4 of 1970) the National Oceanic and Atmospheric Administration (NOAA).

Establishes: (1) a Council on Ocean Stewardship; and (2) a Presidential Panel of Advisers on Oceans and Climate.

Requires the head of each federal agency that undertakes, authorizes, or funds an activity that affects U.S. ocean or coastal waters or resources to make a certification that such action will not harm the marine ecosystem.

Directs the Administrator to develop and maintain a coordinated offshore permit program for certain non-extractive activities in federal waters.

Establishes: (1) the Marine Resources Trust Fund; (2) a Committee on Ocean Science, Education, and Operations; and (3) a National Ocean Science and Technology Scholarship Program.

Deep Sea Coral Protection Act - Requires the Administrator to: (1) research and map deep sea corals and sponges; and (2) compare areas open to bottom-tending mobile fishing gear with areas designated as a Coral Management Area (CMA).

Authorizes the President to permit the Administrator to identify, with foreign entities, areas in international waters that would benefit from additional protection for deep sea corals and deep sea sponges.

Amends the Magnuson-Stevens Fishery Conservation and Management Act to establish a habitat protection program to protect seafloor habitats from the adverse impacts of bottom-tending mobile fishing gear and any other gear or practice that damages seafloor habitat.

Requires the Secretary to prepare and provide guidance for the development of Fisheries Ecosystem Plans.

Requires fishery management plans to: (1) establish and implement a bycatch monitoring and minimization plan; and (2) account for all direct and indirect sources of fishing mortality (including bycatch mortality) in stock assessments, in determining the maximum sustainable yield for the fishery, in establishing total allowable catch and other catch limits necessary to achieve the optimum yield, and in counting the catch.

Cetacean and Sea Turtle Conservation Act of 2005 - Directs the Secretary to enter into negotiations with countries that engage in commercial fishing operations that adversely impact cetaceans or sea turtles that result in agreements requiring such countries to reduce bycatch of such animals to at least sustainable levels.

Provides grants to persons to carry out research and development (R&D) of appropriate fishing gear and methods for use in oceans inhabited by cetaceans or sea turtles.

Revises individual fishing quota provisions to provide for establishment of a fishing quota system through a fishery management plan or amendment. Requires that such a plan: (1) include conservation management measures; (2) establish procedures for a Regional Fishery Management Council (or the Secretary) to review the quota system; (3) allocate, review, and limit or terminate quota shares in accordance with this Act; and (4) not require shares to be held by a person engaged in personal-use fishing, provided the plan designates a separate portion of the allowable catch for such purposes. Requires a Council to make a fair allocation of the total allowable catch limit as quota shares among existing categories of vessels, fishing gear types, or other appropriate qualifiers. Sets forth certain requirements for the allocation, transfer, or termination of a share issued under such a system.

Fisheries Science and Management Enhancement Act of 2005 - Requires each science and statistical committee established by a Council to include a fishery and marine science subcommittee to determine biological catch limits that will prevent overfishing in a fishery and any protections required for threatened or endangered species.

Amends the Marine Mammal Protection Act of 1972 to authorize the Secretary to establish a gear research mini-grant program for developing new types of fishing gear designed to eliminate or reduce the incidental taking of marine mammals.

Establishes a Coastal and Estuarine Land Protection Program.

Establishes a Community-Based Restoration Program.

Amends the National Flood Insurance Act of 1968 to require the Director of the Federal Emergency Management Agency (FEMA) to develop criteria designed to help prevent development and substantial redevelopment in coastal areas.

Establishes the NOAA National Office of Education.

Ballast Water Management Act of 2005 - Amends the Nonindigenous Aquatic Invasive Species Prevention and Control Act of 1990 to revise certain aquatic invasive species prevention requirements to: (1) apply them to certain U.S. vessels and to certain foreign vessels that are en route to, or have departed from, a U.S. port; and (2) establish ballast water and sediment management standards for vessels of the armed forces.

Sets forth protocols for the early detection and monitoring of recently established aquatic invasive species in U.S. waters.

Requires certain administering agencies to conduct a marine and freshwater research program to assess rates of, patterns of, and conditions surrounding introductions of nonidigenous aquatic species in aquatic ecosystems.

Requires the Invasive Species Council to coordinate with the Aquatic Invasive Species Task Force to combat aquatic invasive species. Requires the Task Force, the Council, and the Secretary of State to ensure that international efforts to prevent and control aquatic invasive species are coordinated with U.S. policies.

Amends the Federal Water Pollution Control Act to require the Administrator to: (1) conduct a program to monitor aquatic sediment quality; and (2) promulgate sediment quality criteria and standards protective of the most sensitive aquatic species at their most sensitive life stages.

Requires a state whenever it has reviewed or adopted new water standards to adopt certain advanced wastewater treatment standards for the removal of nutrients from discharges into marine and estuarine water and freshwater.

Authorizes a person to file a civil suit against any person (including the government) in U.S. district court for violations of this Act.