Energy and Water Development and Related Agencies Appropriations Act, 2009 - Title I: Corps of Engineers-Civil - Makes FY2009 appropriations for: (1) the U.S. Army Corps of Engineers for civil functions pertaining to rivers and harbors, flood and storm damage reduction, shore protection, and aquatic ecosystem restoration; (2) general investigations and construction; (3) flood damage reduction for the Mississippi River alluvial valley below Cape Girardeau, Missouri; (4) operation and maintenance expenses; (5) administration of laws pertaining to regulation of navigable waters and wetlands; (6) cleanup of contamination from sites in the United States resulting from work performed as part of the early atomic energy program; (7) flood, hurricane, and natural disasters emergency operations; (8) general administration of the civil works program in the headquarters of the Corps; and (9) the Office of Assistant Secretary of the Army (Civil Works).
(Sec. 102) Prohibits the use of funds to implement any pending or future competitive sourcing actions under OMB Circular A-76 or High Performing Organizations for the Corps of Engineers.
(Sec. 105) Modifies or sets forth requirements or prohibitions regarding the funding of projects in Colorado, Kentucky, Louisiana, New Mexico, and South Dakota.
Title II: Department of the Interior - Makes FY2009 appropriations to the Department of the Interior for: (1) the Central Utah Project; and (2) the Bureau of Reclamation, including for management, development, and restoration of water and related natural resources, the Central Valley Project Restoration Fund, California Bay-Delta restoration, and policy and administration in the Office of the Commissioner, the Denver office, and offices in the five regions of the Bureau of Reclamation.
(Sec. 201) Prohibits the use of funds to determine the final point of discharge for the interceptor drain for the San Luis Unit until development by the Secretary of the Interior and the state of California of a plan, conforming to California water quality standards, to minimize any detrimental effect of the San Luis drainage waters. Requires the costs of the Kesterson Reservoir Cleanup Program and the San Joaquin Valley Drainage Program to be classified as reimbursable or nonreimbursable and collected until fully repaid. Makes any future US obligations relating to drainage for that Unit fully reimbursable by Unit beneficiaries.
(Sec. 205) Directs the Secretary to establish and maintain an Executive Committee of the Middle Rio Grande Endangered Species Collaborative Program.
Title III: Department of Energy - Makes FY2009 appropriations to the Department of Energy (DOE) for expenses related to: (1) energy efficiency and renewable energy; (2) electricity delivery and energy reliability; and (3) nuclear energy.
Transfers specified amounts previously designated for clean coal technology to fossil energy research and development.
Makes FY2009 appropriations for: (1) fossil energy research and development; (2) naval petroleum and oil shale reserve activities, (3) the Strategic Petroleum Reserve; (4) the Northeast Home Heating Oil Reserve; (5) the Energy Information Administration; (6) non-defense environmental cleanup; (7) the Uranium Enrichment Decontamination and Decommissioning Fund; (8) science activities; and (9) nuclear waste disposal, including specified funds designated for the state of Nevada.
Makes FY2009 appropriations for: (1) the Title 17 Innovative Technology Loan Guarantee Program; (2) salaries and expenses for departmental administration; (3) the Office of Inspector General; (4) atomic energy defense weapons; (5) defense nuclear nonproliferation; (6) naval reactors; (7) the Office of the Administrator in the National Nuclear Security Administration; (8) atomic energy defense environmental cleanup; (9) plant and capital equipment necessary for atomic energy defense, other defense activities, and classified activities; and (10) defense nuclear waste disposal.
Makes FY2009 appropriations for operation and maintenance of: (1) the Southeastern, Southwestern, and Western Area Power Administrations; (2) the Falcon and Amistad Dam hydroelectric facilities; and (3) the Federal Energy Regulatory Commission (FERC).
(Sec. 301) Amends the USEC Privatization Act to: (1) declare that it is U.S. policy to support the continued downblending of highly enriched uranium of weapons originating in the Russian Federation; and (2) set forth limitations on the importation into the United States of low-enriched uranium that is produced in the Russian Federation.
(Sec. 306) Prohibits the use of Bonneville Power Administration funds to enter into any agreement to perform energy efficiency services outside the legally defined Bonneville service territory, with the exception of services provided internationally, including services provided on a reimbursable basis, unless the Administrator certifies in advance that such services are not available from private sector businesses.
(Sec. 307) Requires DOE: (1) when it makes a user facility available to universities or other potential users, or seeks their input on significant user facility characteristics or equipment, to ensure broad public notice of such availability or input need; and (2) to employ full and open competition in selecting a university or other potential user as a formal partner in the establishment or operation of a user facility.
(Sec. 308) Deems any funds appropriated by this or any other Act, or made available by the transfer of funds in this Act, for intelligence activities to be specifically authorized by Congress for purposes of the National Security Act of 1947 during FY2009, until the enactment of the Intelligence Authorization Act for FY2009.
(Sec. 309) Authorizes the use of specified funds by government-owned, contractor-operator operated laboratories for laboratory-directed research and development.
(Sec. 313) Directs the Secretary of Energy, along with the Administrator of the National Nuclear Security Administration and the Chairman of the Nuclear Regulatory Commission (NRC), to establish an Integrated University Program.
(Sec. 314) Requires facilities at Sandia National Laboratories and Los Alamos National Laboratory, New Mexico, to be named in honor of Senator Pete V. Domenici.
Title IV: Independent Agencies - Makes FY2009 appropriations to: (1) the Appalachian Regional Commission; (2) the Defense Nuclear Facilities Safety Board; (3) the Delta Regional Authority; (4) the Denali Commission; (5) the NRC, including its Office of Inspector General; (6) the Nuclear Waste Technical Review Board; and (7) the Office of the Federal Coordinator for Alaska Natural Gas Transportation Projects.
Title V: General Provisions - (Sec. 501) Prohibits the use of funds appropriated by this Act to influence congressional action on legislation or appropriation matters pending before Congress, with an exception.
(Sec. 502) Prohibits the transfer of funds made available by this Act to any federal department, agency, or instrumentality, except pursuant to a transfer made by, or transfer authority provided in, this Act or any other appropriation Act.