Water Resources Development Act of 2003 - Title I: Water Resources Projects - (Sec. 1001) Authorizes the Secretary of the Army, subject to specified conditions, to carry out specified projects for: (1) environmental restoration in Arizona; (2) flood damage reduction and environmental restoration in California; (3) environmental restoration in Colorado; (4) environmental restoration in Illinois; (5) hurricane and storm damage reduction in Louisiana; (6) environmental restoration and protection in Maryland; (7) hurricane and storm damage reduction and environmental restoration in New Jersey; (8) navigation and environmental restoration in Texas; and (9) bridge replacement in Virginia. Authorizes the Secretary, subject to a favorable final report, to carry out specified projects for: (1) environmental restoration in California; (2) storm damage reduction in California; (3) environmental restoration in Maryland; (4) hurricane and storm damage reduction in New Jersey; and (5) flood damage reduction in Washington. (Sec. 1002) Directs the Secretary to conduct studies of, and authorizes the Secretary to carry out (if determined feasible after the study), specified projects for: (1) flood damage reduction in Arkansas, California, Illinois, Kentucky, Massachusetts, Michigan, Minnesota, Missouri, New Jersey, New York, Pennsylvania, and South Carolina; (2) emergency streambank protection in Arkansas, Illinois, Minnesota, Missouri, New Jersey, and New York; (3) navigation in Arkansas, Florida, Illinois, Louisiana, Michigan, New York, and Washington; (4) environmental quality improvement in Missouri; (5) aquatic ecosystem restoration in Arizona, California, Florida, Georgia, Georgia and Alabama, and Idaho; (6) shoreline protection in Alaska; and (7) snagging and sediment removal in New York. Title II: General Provisions - (Sec. 2001) Amends the Water Resources Development Act (WRDA) of 1996 to extend through 2004 the authority for establishing an annual pass of $10 or less for the use of recreational facilities at water resources projects of the U.S. Army Corps of Engineers (Corps). (Sec. 2002) Amends the WRDA of: (1) 1986 to prohibit the Secretary from soliciting from non-Federal interests the costs of projects or measures in excess of the assigned non-Federal share; (2) 1986 to increase from 45 to 53 feet the depth of harbor projects for which non-Federal interests must pay the maximum share of construction and operations costs; and (3) 2000 to extend through FY 2005 the Secretary's authority to accept and expend non-Federal funds to expedite the evaluation of permits. (Sec. 2005) Extends for four years the national shoreline erosion control development and demonstration program. Extends by three years the program's planning, design, and construction phase. Authorizes the Secretary to: (1) enter into a cost-sharing agreement with a non-Federal interest in connection with the program; and (2) pay all or a portion of the costs of removing a project, or project element, if determined to be detrimental to the environment, private property, or public safety. Increases the program's authorization of appropriations. (Sec. 2006) Amends the: (1) Flood Control Act of 1970 to revise generally the content of partnership agreements for water resources projects under such Act; and (2) WRDA of 1986 to authorize the payment of damages (currently, only injunctions) in the case of the breach of local water resource project cooperation agreements. Requires agreements entered into: (1) under the former Act to further partnership and cooperative arrangements with non-Federal interests; and (2) after January 1, 2005, under such Act to be entered into (with an exception) with the district engineer for the district in which the project will be carried out. Directs the Army Chief of Engineers to ensure that each district engineer has made available on the Internet all current partnership agreements. (Sec. 2007) Authorizes the Secretary to provide to State and local governments assessment, planning, and design assistance for the remediation, restoration, or reuse of areas which will contribute to improving water quality or conserving water and related resources of drainage basins and watersheds. Requires a non-Federal share of 50 percent. Authorizes appropriations. (Sec. 2008) Requires the laws concerning rivers and harbors, flood control, beach erosion, and other water resources development enacted after November 8, 1966, and before January 1, 2004, to be compiled and printed for the use of the Department of the Army, Congress, and the public. (Sec. 2009) Amends the WRDA of 1996 to authorize the Secretary to enter into cost-sharing agreements under governmental partnerships for dredged material disposal. (Sec. 2010) Requires the preferential use of mitigation banks in carrying out projects that involve wetlands mitigation. (Sec. 2011) Authorizes the Secretary, in conducting a study of harbor and navigation improvements, to recommend a project without the need to demonstrate that the project is justified solely by national economic development benefits if the Secretary determines that the project would involve a remote or subsistence harbor (a harbor that is at least 70 miles away from the community served by the project or that transports over 80 percent of the goods consumed by the community served). (Sec. 2012) Amends the WRDA of 1992 to authorize the Secretary to carry out projects for the beneficial use of dredged material. Authorizes annual appropriations. Authorizes the Secretary, under such projects, to: (1) provide for regional sediment management planning; and (2) give priority to two specified projects in North Carolina and New York. (Sec. 2013) Amends the WRDA of 1986 to direct the Secretary to waive local cost-sharing requirements up to $500,000 (currently $200,000) for all studies and projects in American Samoa, Guam, the Northern Mariana Islands, and the Virgin Islands (current law), the Commonwealth of Puerto Rico, and certain Indian lands. (Sec. 2017) Amends the WRDA of: (1) 1999 to make permanent the authority to withhold certain recreation user fees for recreation area repair, maintenance, and other costs; (2) 1986 to add a specified California project to a watershed and river basis assessment program, and to reduce from 50 to 25 percent the non-Federal share of costs of such assessments; and (3) 2000 to include within a tribal partnership program lands located within the jurisdictional area of an Oklahoma Indian tribe and recognized as eligible for trust land status. (Sec. 2018) Directs the Secretary to expedite any actions for emergency flood damage reduction for lands qualifying for major disaster assistance under the Robert T. Stafford Disaster and Emergency Relief Act. (Sec. 2021) Authorizes the Secretary to treat as a separable project element an element that would advance a primary mission of the Corps (with cost limits). (Sec. 2022) Amends the Rivers and Harbors Act to include any required planning, engineering, design, construction, operation, and maintenance within work authorized to be prosecuted on canals, rivers, and harbors. (Sec. 2023) Authorizes the Secretary to enter into wildfire firefighting contracts with State and local governmental entities. (Sec. 2024) Authorizes the Secretary to allow a non-Federal interest credit (with limitations) for the cost of materials and in-kind services (but not including construction) provided for implementation of a project. (Sec. 2025) Amends the WRDA of 1974 to authorize the Secretary to provide technical assistance to a governmental agency or non-Federal interest in managing water resources. Authorizes annual appropriations. (Sec. 2026) Authorizes the Secretary to establish centers to provide specialized planning expertise for water resources projects to be carried out by the Secretary to enhance and supplement the capabilities of the Corps districts. (Sec. 2027) Directs the Secretary, upon the request of a non-Federal interest, to establish a schedule for consolidating Federal, State, local agency, and Indian tribe environmental assessments, project reviews, and issuance of all permits for the construction or modification of a project. Requires: (1) notice of such request in the Federal Register; (2) implementation of a scheduling agreement and agreement revisions; (3) reimbursement of costs associated with agreement implementation; and (4) a report to Congress on the time required for issuance of all necessary permits. (Sec. 2028) Requires the Secretary to develop and implement a coordinated water resources development project review process. Requires: (1) all necessary project reviews, assessments, etc. to be conducted concurrently and completed within an established time period; and (2) notification of the failure of a Federal, State, or local agency, Indian tribe, or non-Federal interest to meet such deadline (requiring reports from such party on why the deadline was not met). Directs the Secretary to: (1) define the purpose and need for the proposed project; and (2) determine which alternatives are reasonable and may be reasonably anticipated to meet such purposes and needs. Requires the Secretary to develop and publish a list of categorical exclusions from the requirement that an environmental assessment or impact statement be prepared under the National Environmental Policy Act of 1969 for water resources projects. Requires the Chief of Engineers to: (1) establish benchmarks for determining appropriate lengths of time for a project feasibility study and its associated review process; and (2) use of such benchmarks as a management tool to make the feasibility study process more efficient in all Corps districts. (Sec. 2029) Amends the WRDA of 1986 to add specified lakes and ponds in Illinois, New Jersey, New York, and North Carolina to the lakes remediation program. (Sec. 2030) Amends the WRDA of 1986 to authorize the Secretary, when it is not technically feasible to complete mitigation of a project's fish and wildlife losses by the last day of a project's construction (current law), to complete such mitigation as expeditiously as possible, but not later than the last day of the first fiscal year beginning after the last day of construction of the project or separable project element thereof. Outlines mitigation plan contents. Directs the Secretary to report to specified congressional committees on the construction status of projects that require such mitigation and the status of such mitigation. (Sec. 2031) Authorizes the Secretary, in order to expedite the cost-effective design and construction of wetlands restoration that is part of an authorized project, to enter into cooperative agreements with nonprofit organizations with expertise in such restoration. Limits the amount of payments to such organizations. (Sec. 2032) Requires, as the Federal objective of any feasibility study for a water resource project, to maximize the net national economic development or ecosystem restoration benefits associated with the project. Authorizes the Secretary to select a project alternative that does not maximize such benefits if there is an overriding reason based upon other Federal, State, local, or international concerns. Provides examples of possible overriding reasons with respect to certain types of projects. Authorizes the Secretary to identify additional benefits with respect to a project, and to recommend construction of a separate project or element to achieve those benefits. Requires feasibility studies for flood damage reduction projects to include a calculation of benefits and costs associated with the project. (Sec. 2033) Requires project studies to be subject to peer review by an independent panel of experts if the project has an estimated total cost of more than $50 million, and is not determined by the Chief of Engineers to be exempt from such peer review. Outlines situations under which a project study may be: (1) subject to discretionary peer review, including when the Chief determines that a project study is controversial; and (2) excluded from peer review, including when the project is determined to be non-controversial or having only negligible adverse impacts on scarce or unique resources. Authorizes the appeal of a decision whether to peer review a project. Requires the Chief to determine the timing of a peer review. Provides for the establishment of panels to conduct necessary peer reviews, requiring such panels to generally complete such reviews within 180 days. Requires peer review reports to be made public and transmitted to Congress. Limits panel costs. Requires a report from the Chief to Congress on the implementation of peer review requirements. (Sec. 2034) Authorizes the Secretary to provide assistance to: (1) the University of Tennessee, Knoxville, for establishment and operation of the Southeastern Water Resources Institute to study sustainable development and utilization of water resources in the southeastern United States; and (2) Lewis and Clark Community College, Illinois, for the Great Rivers National Research and Education Center, a collaborative effort for the study of river ecology, developing watershed and river management strategies, and educating students and the public on river issues. Authorizes appropriations. Title III: Project-Related Provisions - (Sec. 3001) Modifies specified projects for navigation, flood control, flood damage reduction, aquatic ecosystem restoration, environmental quality improvement, shore protection, flood damage reduction and restoration, floodway systems, mitigation of fish and wildlife losses, hurricane-flood protection, emergency streambank and shoreline protection, and environmental restoration in Alaska, Arizona, Arkansas, California, Florida, Idaho, Illinois, Indiana, Kentucky, Louisiana, Maine, Michigan, Minnesota, Mississippi, Missouri, Nebraska, New Mexico, New York, New York and New Jersey, Oklahoma, Oregon, Pennsylvania, Tennessee, Texas, Virginia, Washington, West Virginia, Wisconsin, and the Mississippi River headwaters reservoirs. (Sec. 3080) Authorizes the Secretary to take necessary action to prevent shoreline erosion along a specified length of the east shore of Raystown Lake, Pennsylvania. (Sec. 3098) Continues authorized projects in Fall Harbor, Massachusetts, and Agana River, Guam. (Sec. 3099) Reauthorizes (if determined feasible) the projects for navigation at Menominee River and Harbor, Michigan and Wisconsin, and Manitowoe Harbor, Wisconsin. (Sec. 3100) Deauthorizes navigation projects for: (1) Bridgeport Harbor, Connecticut; (2) Norwalk Harbor, Connecticut; (3) Chicago River and Harbor, Illinois; (4) Muscatine, Iowa; (5) Falmouth Harbor, Massachusetts; (6) Island End River, Massachusetts; and (7) City Waterway, Tacoma, Washington. Designates a portion of the New London Harbor, Connecticut, as an anchorage area. Deauthorizes water resources projects in California, Florida, Indiana, Iowa, Kentucky, Louisiana, Louisiana and Texas, Massachusetts, Michigan, Mississippi, Montana, Nebraska, New York, North and South Carolina, Ohio, Oklahoma, Oregon, Rhode Island, Tennessee, Colorado and Texas, Texas, and West Virginia. (Sec. 3101) Directs the Secretary to convey to the Geary County Fire Department certain lands in Geary County, Kansas. Amends the WRDA of 1996 to redesignate the recipient of a certain land conveyance near Boardman, Oregon. (Sec. 3102) Extinguishes certain reversionary interests and use restrictions relating to: (1) the transfer of specified parcels in Nez Perce County, Idaho; and (2) recreation and camping purposes at Old Hickory Lock and Dam, Tennessee. (Sec. 3103) Authorizes the Secretary to undertake a land exchange and related disposal and acquisition of other lands in the area of Allatoona Lake, Georgia. Title IV: Studies - (Sec. 4001) Amends the WRDA of 1999 to allow the non-Federal interest to provide up to 100 percent of its required share with respect to the John Glenn Great Lakes Basin program in the form of in-kind contributions. (Sec. 4002) Sets forth provisions modifying, requiring, or setting forth additional requirements for specified studies associated with projects in Alabama, Alaska, Arkansas, California, Georgia, Illinois, Kentucky, Louisiana, Massachusetts, Michigan, Mississippi, New Mexico, New Jersey and New York, Oklahoma, Oregon, Pennsylvania, South Carolina, Texas, Utah, Washington, West Virginia, Wisconsin, Lake Erie dredged material disposal sites, and the Upper Mississippi River and Illinois Waterway in Illinois, Iowa, Minnesota, Missouri, and Wisconsin. Title V: Miscellaneous Provisions - (Sec. 5001) Makes the Secretary responsible, under certain conditions, for maintenance of specified navigation channels in Texas, Tennessee, and Wisconsin. Directs the Secretary to remove sunken vessels and other debris from a channel in the Sabine-Neches Waterway, Texas. (Sec. 5002) Authorizes the Secretary to provide technical, planning, and design assistance to non-Federal interests for carrying out watershed management, restoration, and development projects at specified locations in Alabama, California, Colorado, Illinois, Massachusetts, New Jersey, Pennsylvania, Louisiana, and New York. Requires a non-Federal share of 50 percent. Authorizes appropriations. (Sec. 5003) Authorizes the Secretary to provide assistance to enhance dam safety at specified dams in Georgia, Idaho, New Jersey, New York, and Oklahoma. Expresses the sense of Congress that the Secretary should work to immediately remedy the situation at Fern Ridge Dam, Oregon, caused by rapid deterioration. Authorizes appropriations. (Sec. 5004) Directs the Secretary, under certain conditions, to undertake structural integrity evaluations at specified flood damage reduction projects in Arkansas, Pennsylvania, and Tennessee. (Sec. 5005) Amends the WRDA of: (1) 1999 to add certain areas as flood mitigation priority areas; and (2) 1992 to authorize additional monetary assistance under current projects. (Sec. 5007) Directs the Secretary to expedite completion of reports and, if determined feasible: (1) expedite completion of construction for specified projects in Maryland, New York, and Illinois; and (2) proceed directly to project preconstruction, engineering, and design for specified projects in California, Florida, Louisiana, Maryland, and Michigan. Provides special rules with respect to certain projects. (Sec. 5009) Authorizes the Secretary to provide assistance to assess the water resources and related needs of river basins and watersheds of the southeastern United States. (Sec. 5010) Amends the WRDA of: (1) 1986 to allow the non-Federal interest under the Upper Mississippi River environmental management program to provide its required non-Federal share in in-kind contributions; (2) 1999 to extend through 2015 the authorization of appropriations for the Missouri and Middle Mississippi Rivers enhancement project; (3) 2000 to include representatives of rural water systems within the membership of the Missouri River Trust; (4) 2000 to allow non-Federal interests to provide up to 100 (currently 50) percent of their cost share for Great Lakes fishery and ecosystem restoration in the form of in-kind contributions; and (5) 1996 to increase the authorization of appropriations for the Chesapeake Bay environmental restoration and protection program. (Sec. 5014) Requires the Division Engineer, North Atlantic Division, Corps of Engineers, beginning in FY 2002 and thereafter, to be the ex officio U.S. member under the Susquehanna River Basin Compact and the Delaware River Basin Compact. Directs the Secretary to enter into an agreement with the Delaware River Basin Commission to provide temporary water supply and conservation storage at the Francis E. Walter Dam in Pennsylvania during any period in which that Commission has determined that a drought warning or drought emergency exists. (Sec. 5016) Directs the Secretary to: (1) review the navigation and aquatic ecosystem restoration components of the Riverfront and Downtown Master Plan for Montgomery, Alabama, and carry out such components if determined feasible; (2) design and construct the locally preferred plan for flood protection at Pinhook Creek, Alabama; (3) expedite the study for the Akutan Small Boat Harbor, Alaska; (4) make necessary dike repairs at Fort Yukon, Alaska; (5) assume responsibility for long-term maintenance and repair of the Lowell Creek Tunnel, Alaska; and (6) carry out on an emergency basis the removal of rubble, sediment, and rock that are impeding the entrance to the St. Herman Harbor, Kodiak, Alaska. (Sec. 5018) Amends the WRDA of 1999 to increase the authorization of appropriations for the provision of environmental assistance to non-Federal interests in Alaska. (Sec. 5023) Authorizes the Secretary to perform operation, maintenance, and rehabilitation of authorized and completed levees on the White River between Augusta and Clarendon, Arkansas. (Sec. 5024) Directs the Secretary to accept certain contributions of cash and lands as fulfilling the non-Federal cost sharing responsibilities in connection with the project for flood control, Helena and vicinity, Arkansas. (Sec. 5025) Requires the Secretary to conduct a study of shore damage in the vicinity of Loomis Landing, Arkansas. (Sec. 5026) Modifies the McClellan-Kerr Arkansas River navigation and comprehensive development project to authorize a project depth of 12 feet in the States of Arkansas and Oklahoma. (Sec. 5027) Requires the Secretary to conduct a study of increased siltation and streambank erosion in the St. Francis River basin, Arkansas and Missouri. (Sec. 5028) Amends the WRDA of: (1) 1992 to direct the Secretary to provide certain non-Federal share cost credit in connection with a desalination project at Cambria, California, and water recharge and conjunctive use projects in East San Joaquin County, California; (2) 2000 to provide for the conduct of project planning, study, design, and construction for California flood damage reduction projects at the Contra Coastal Canal and the Mallard Slough; and (3) 1992 to increase the authorization of appropriations for water supply and regional water recycling and conservation projects in the Sacramento, California, area. (Sec. 5031) Authorizes the Secretary to establish a program to provide environmental assistance to non-Federal interests in Placer and El Dorado Counties, California. Requires partnership agreements. Makes the Federal share 75 percent. Provides certain credits for the non-Federal interests. Authorizes appropriations. (Sec. 5033) Authorizes the Secretary to: (1) transfer title to the Bascule Bridge to the city of West Sacramento, California; and (2) participate in the construction of a replacement bridge following the removal of such bridge. Authorizes appropriations. (Sec. 5034) Directs the Secretary to carry out the project for the removal of Wharf 5 and associated pilings at Pier 70 in San Francisco, California. Authorizes appropriations. (Sec. 5035) Requires the Secretary, unless it is found not to be in the public interest, to declare a specified portion of the San Francisco waterfront area to be non-navigable waters (and therefore eligible for Federal improvement). (Sec. 5036) Directs the Secretary to conduct and complete certain studies, complete work, and participate in critical ecosystem restoration projects at the San Pablo Bay watershed and the Suisun Bay Marsh, California. Provides for cost-sharing and credits for non-Federal interests. Authorizes appropriations. (Sec. 5037) Directs the Secretary to reevaluate the feasibility of certain elements of a project for flood control, Stockton, California, and, if determined feasible, to reimburse the non-Federal interests for the Federal share of such costs. (Sec. 5038) Authorizes the Secretary to establish a program to provide environmental assistance to non-Federal interests in the Upper Klamath Basin, California. Requires partnership agreements. Makes the Federal share 75 percent. Provides certain credits for the non-Federal interests. Authorizes appropriations. (Sec. 5039) Designates the western breakwater for the project for navigation, New Harbor, Connecticut, as the Charles Hervey Townshend Breakwater. (Sec. 5040) Amends the WRDA of 2000 to include the project for aquifer storage and recovery, Hillsboro and Okeechobee Aquifer, Florida, within a comprehensive Florida Everglades restoration plan. Increases the authorization of appropriations in order to cover such project. Amends the WRDA of 1996 to increase the authorization of appropriations for critical Everglades restoration projects. (Sec. 5041) Amends the Miscellaneous Appropriations Act, 2001 to direct the Secretary to provide certain non-Federal share credit with respect to a project for water quality improvements in the Florida Keys. (Sec. 5042) Authorizes the Secretary to: (1) carry out necessary repairs for the Lake Worth bulkhead replacement project in West Palm Beach, Florida; (2) assist local interests in the planning, design, and construction of facilities at the Lake Lanier Olympic Center, Georgia; and (3) carry out the Riley Creek Restoration Area operation plan. (Sec. 5045) Authorizes the Secretary to participate in the reconstruction of certain Illinois Drainage District flood protection projects if the Secretary determines that such reconstruction is not required as a result of improper operation and maintenance of the project by the non-Federal interest. Authorizes appropriations. (Sec. 5046) Amends the WRDA of 1992 to direct the Secretary to provide certain non-Federal share credit with respect to a project for environmental resource protection and development in Cook County, Illinois. (Sec. 5047) Directs the Secretary to develop a comprehensive plan for restoring, preserving, and protecting the Kaskaskia River Basin, Illinois, including the development of new technologies and innovative approaches. Requires: (1) a plan report to Congress; and (2) after such plan, any necessary additional studies and analyses. Requires the Secretary's recommendations to be consistent with applicable State water quality standards. Requires: (1) public participation in plan development; and (2) plan coordination with specified programs and initiatives. Requires a 35 percent non-Federal cost share and provides for the use of in-kind contributions. (Sec. 5048) Directs the Secretary to carry out a project for flood damage reduction, if feasible, at Natalie Creek, Illinois. (Sec. 5049) Authorizes the Secretary to carry out the project for Peoria riverfront development in Peoria, Illinois. (Sec. 5050) Amends the WRDA of: (1) 2000 to extend through 2010 the authorization of appropriations for the Illinois River Basin restoration program; and (2) 1992 to increase the authorization of appropriations for, and add certain areas to, water-related infrastructure projects in the Calumet region, Indiana. (Sec. 5051) Authorizes the Secretary to establish a program to provide environmental assistance to non-Federal interests in Southwest Illinois. Requires partnership agreements. Makes the Federal share 75 percent. Provides certain credits for the non-Federal interests. Authorizes appropriations. (Sec. 5053) Directs the Secretary to convey the remaining water supply storage allocation in Rathbun Lake, Iowa, to the Rathbun Regional Water Association, and requires the Association to pay 100 percent of allocation costs. (Sec. 5054) Directs the Secretary to continue to charge certain water supply storage and maintenance fees at reservoirs within the Cumberland River basin, Kentucky. (Sec. 5055) Directs the Secretary to conduct a study of flood damage along Mayfield Creek and its tributaries, Kentucky, to determine if such damage is federally caused, and, if so, to mitigate such damage. (Sec. 5056) Directs the Secretary to rebuild the structure that is impeding high-water flows on the North Fork of the Kentucky River in Breathitt County, Kentucky. (Sec. 5057) Amends the WRDA of 1996 to allow ten percent of each year's funds authorized for a program of environmental assistance to non-Federal interests in southern and eastern Kentucky to be used by the Corps for administrative expenses. (Sec. 5058) Directs the Secretary to develop a comprehensive plan for protecting, preserving, and restoring the Coastal Louisiana Ecosystem. Requires: (1) plan submission to Congress by July 1, 2004; and (2) the Secretary to integrate such plan with ongoing Federal and State projects and activities. Provides a non-Federal cost share of 50 percent. Establishes the Coastal Louisiana Ecosystem Protection and Restoration Task Force to undertake specified activities toward plan development and implementation. (Sec. 5059) Amends the WRDA of: (1) 1992 to increase the authorization of appropriations for an environmental infrastructure project at Baton Rouge, Louisiana; and (2) 1999 to add an additional authorized purpose under a West Baton Rouge waterfront and riverine restoration project. (Sec. 5062) Authorizes the Secretary: (1) in carrying out a study to address shoreline erosion and related conditions in the Chesapeake Bay area, to carry out pilot projects to demonstrate the feasibility of alternative measures to address sediment loss to such Bay; and (2) to provide technical assistance to the Secretary of Agriculture in carrying out the related Conservation Corridor Demonstration Program. (Sec. 5064) Amends the WRDA of 1999 to increase the authorization of appropriations for the repair and rehabilitation of seawalls along the Detroit River, Michigan. (Sec. 5066) Directs the Secretary to: (1) carry out aquatic ecosystem restoration projects for the St. Clair River and Lake St. Clair, Michigan; and (2) conduct a study for a project for emergency streambank protection near Crookston, Minnesota, and, if determined feasible, carry out such project. (Sec. 5068) Amends the WRDA of 1992 to include Crow Wing and Mille Lacs Counties, Minnesota, under a wastewater infrastructure project. (Sec. 5069) Amends the WRDA of 1999 to: (1) revise the definition of "northeastern Minnesota" for purposes of a pilot program to provide environmental assistance to non-Federal interests in such area; and (2) repeal a limitation on credit given for design work performed by such non-Federal interests. Directs the Secretary to reimburse the non-Federal interest for the project for environmental infrastructure, Biwabik, Minnesota, for certain planning, design, and construction costs. (Sec. 5070) Amends the WRDA of 1992 to increase the authorization of appropriations for an environmental project in Desoto County, Mississippi. (Sec. 5071) Directs the Secretary, in carrying out projects for the protection, restoration, and creation of aquatic and ecologically related habitats in Harrison, Hancock, and Jackson Counties, Mississippi, to accept any portion of the non-Federal share in the form of in-kind contributions. (Sec. 5072) Authorizes the Secretary, as part of the operation and maintenance of the project for the Mississippi River (Regulating Works), to carry out activities to restore and protect fish and wildlife habitat in the middle Mississippi River system. (Sec. 5073) Amends the WRDA of 1992 to: (1) increase the authorization of appropriations for a project to eliminate or control sewer overflows in the city of St. Louis, Missouri; (2) redesignate recipients of Federal assistance to develop an environmental improvement program for the Hackensack Meadowlands area of New Jersey and to increase the authorization of appropriations for such program; and (3) revise requirements for a data collection and monitoring program of coastal processes for a specified portion of the Atlantic Coast of New York and to increase the authorization of appropriations for such program. (Sec. 5074) Directs the Secretary to provide assistance to address floating and partially submerged debris on the Delaware River downstream from Trenton, New Jersey. (Sec. 5077) Directs the Secretary to: (1) give priority to work in College Point, New York City, under a project for environmental dredging in the United States; (2) provide certain credit toward the non-Federal share of a project for ecosystem restoration in Flushing Bay and Creek, New York City; and (3) review a report concerning waterfront development at Gateway Point, North Tonawanda, New York, and, if determined feasible, carry out the shoreline stabilization, recreation, and public access components of such development. (Sec. 5080) Authorizes the Secretary to carry out a navigation project at Little Neck Bay, Kings Point, New York, sufficient to permit the safe operation of a specified vessel at all tide levels. (Sec. 5081) Amends the WRDA of 1999 to increase the authorization of appropriations for projects to restore, conserve, and manage Onondaga Lake, New York. (Sec. 5082) Authorizes the Secretary, as part of operation and maintenance of the Buffalo Harbor and River navigation projects, to repair the Times Beach confined disposal facility dike, Buffalo, New York. (Sec. 5083) Directs the Secretary to expedite completion of a revised contract for water supply storage at John H. Kerr Dam and Reservoir, North Carolina. (Sec. 5085) Requires the Secretary, if authorized to carry out a downtown waterfront development project for the Central Riverfront Park, Cincinnati, Ohio, to provide certain credits toward the non-Federal share of such project. (Sec. 5086) Directs the Secretary to upgrade the condition of a road on the Piedmont Lake Dam, Ohio, to meet Ohio standards applicable to public use roads. (Sec. 5087) Amends the WRDA of 1999 to increase the authorization of appropriations for a project to provide environmental assistance to non-Federal interests in Ohio. (Sec. 5088) Sets the amount of the remaining obligation payable to the United States by the Waurika Project Master Conservancy District in connection with a project at Waurika Lake, Oklahoma. (Sec. 5089) Adds Celilo Village, Oregon, to the authorized sites for a project for fishing access improvement along the Columbia River, Oregon. (Sec. 5090) Directs the Secretary to conduct a study for the feasibility of restoring the millrace in Eugene, Oregon. Authorizes appropriations. (Sec. 5091) Directs the Secretary to pay up to $2.5 million to the provider of research and curation support previously provided to the Federal Government as a result of the multipurpose project, John Day Lock and Dam, Lake Umatilla, Oregon and Washington. Authorizes appropriations. (Sec. 5092) Authorizes the Secretary to convey to Lowell School District a specified tract in Lowell, Oregon. (Sec. 5093) Authorizes the Secretary to: (1) rehabilitate the pumps at the project for flood damage reduction, Hagerman's Run, Williamsport, Pennsylvania; and (2) make improvements to the Susquehannock Campground Access Road at Raystown Lake, Pennsylvania. (Sec. 5094) Amends the WRDA of: (1) 1992 to add certain counties to a project for water-related infrastructure projects in northeastern Pennsylvania; (2) 1996 to increase the authorization of appropriations for wetland restoration projects in the Upper Susquehanna River Basin, Pennsylvania and New York; (3) 1992 to increase the authorization of appropriations for water and wastewater infrastructure in specified Pennsylvania counties; and (4) 1992 to increase the authorization of appropriations for, and add wastewater treatment as an authorized purpose to, water supply and distribution projects in specified South Carolina counties. (Sec. 5098) Directs the Secretary to review: (1) a report in connection with a proposed project for flood protection and environmental restoration for Cano Martin Pena, San Juan, Puerto Rico, and, if appropriate, carry out the project; and (2) the project for flood damage reduction, Upper Big Sioux River basin, South Dakota, and, if appropriate, carry out the project. (Sec. 5099) Authorizes the Secretary to: (1) accept specified funds from the Department of the Navy for use in assisting the Beaufort Jasper Water and Sewage Authority, South Carolina, with its plan to consolidate civilian and military wastewater treatment facilities; and (2) provide technical and financial assistance for the removal of the Grace and Pearman Bridges over the Cooper River, South Carolina. Authorizes appropriations for the latter project. (Sec. 5103) Directs the Secretary to: (1) study the Fritz Landing Agricultural Spur Levee, Tennessee, to determine the appropriate extent of levee modifications required to meet Federal standards and to design and construct such modifications; (2) plan, design, and construct upgrades to the existing trail system at the J. Percy Priest Dam and Reservoir, Tennessee; (3) review the aquatic ecosystem component of a specified project in Memphis, Tennessee, and, if determined feasible, authorize the Secretary to carry out such component (with a Federal cost limit); and (4) design and construct the project for flood damage reduction at Town Creek, Lenoir City, Tennessee. (Sec. 5107) Authorizes the Secretary to establish a program to provide environmental assistance to specified counties in East Tennessee. Requires: (1) partnership agreements; and (2) a Federal cost share of 75 percent. Provides certain credits for the non-Federal share of the program. Authorizes appropriations. (Sec. 5108) Authorizes the Secretary, as part of a navigation project for the Tennessee River, to enter into a partnership with a nonprofit entity for the removal of debris from the Tennessee River in the vicinity of Knoxville, Tennessee. Authorizes appropriations. (Sec. 5109) Directs the Secretary to expedite completion of a report for the project for flood damage reduction and other measures in Clear Creek and tributaries, Texas. (Sec. 5111) Directs the Secretary to conduct a study of a project for flood damage reduction in the Harris County watershed, Texas, to determine the feasibility of including flood damage protection for the Texas Medical Center in Houston. Requires study completion by July 1, 2004. Authorizes the Secretary to carry out critical flood damage reduction measures in such watershed. (Sec. 5112) Directs the Secretary to provide certain credit toward non-Federal share costs of the project for flood damage reduction, recreation, and ecosystem restoration, Onion Creek, Texas. (Sec. 5113) Amends the Energy and Water Development Appropriations Act, 1994 to authorize the Secretary to provide a letter of intent to the city of Galveston, Texas, for conveyance of a specified parcel for private development purposes. (Sec. 5114) Amends the WRDA of 1992 to increase the authorization of appropriations for a project for environmental restoration and remediation, Front Royal, Virginia. (Sec. 5115) Authorizes the Secretary to carry out bluff stabilization measures in Richmond National Battlefield Park, Virginia. (Sec. 5116) Directs the Secretary to: (1) conduct a study to determine if increased siltation in Baker Bay and Ilwaco Harbor, Washington, is the result of a Federal navigation project and, if so, to mitigate the situation; (2) provide certain credit toward non-Federal share costs of the project for flood damage reduction, Chehalis River, Washington; (3) place dredged and other suitable material along the Columbia River shoreline of Puget Sound, Washington; and (4) conduct a watershed and river basin assessment for the Lower Kanawha River Basin, West Virginia. (Sec. 5118) Authorizes the Secretary to plan, design, and construct a campground for Bonneville Lake and Dam at Hamilton Island, Washington. (Sec. 5120) Amends the WRDA of 2000 with respect to the project for flood control, Bluestone Lake, West Virginia, to: (1) add an additional year to the authorized period for designing and constructing a hydroelectric generating facility there; (2) make the Tri-Cities Power Authority the owner and operator of the hydropower facilities; (3) direct the Secretary to review the design and construction activities for all features of the hydroelectric project that pertain to dam stability and the release of water from the Bluestone Dam; and (4) require construction of the hydroelectric generating facilities to be coordinated with a dam safety assurance project currently in the design and construction phase. (Sec. 5121) Amends the WRDA of 1996 with respect to the project for flood control, Cheat and Tygart River Basins, West Virginia, to: (1) add as authorized project purposes streambank protection, stormwater management, and channel clearing and modification measures; and (2) increase the authorization of appropriations for such project. (Sec. 5123) Amends the WRDA of: (1) 1999 to remove two counties from a pilot program to provide environmental assistance to non-Federal interests in central West Virginia; and (2) 1992 to include one of the counties so removed within the definition of southern West Virginia for purposes of a similar project. (Sec. 5125) Amends the WRDA of 1996 to add two projects in Texas and one in Minnesota to flood control projects authorized under such Act to be undertaken by non-Federal interests. (Sec. 5126) Authorizes appropriations for the construction of a bridge on the Tanque Verde Creek, Arizona. (Sec. 5127) Amends the WRDA of 1992 to authorize the Secretary to provide specified monetary assistance for water- or wastewater-related infrastructure projects in Louisiana, South Carolina, California, North Carolina, the District of Columbia, Indiana, Nevada, New York, Connecticut, Alabama, Tennessee, the District of Columbia and Maryland, Utah, Mississippi, Texas, and Georgia. (Sec. 5128) Directs the Secretary to conduct a study of, and report to Congress on, the appropriate use of the Federal hopper dredge fleet. (Sec. 5129) Requires U.S. Army Corps of Engineers employees who are paid wages under the "Administrative Provisions" of chapter V of the Supplemental Appropriations Act, 1982 to be allowed to participate in wage surveys to the same extent as Federal prevailing rate employees. (Sec. 5130) Expresses the sense of Congress that, to the extent practicable, all equipment and products purchased with funds made available under this Act should be American-made. Requires the Secretary to so notify recipients of assistance under this Act.