TABLE OF CONTENTS: Title I: Water Resources Projects Title II: Generally Applicable Provisions Title III: Project Modifications Title IV: Studies Title V: Miscellaneous Provisions Water Resources Development Act of 1996 - Title I: Water Resources Projects - Authorizes the Secretary of the Army to carry out specified projects for navigation, flood control, flood and storm damage reduction, environmental preservation and restoration, shoreline erosion protection, hydropower, and hurricane damage reduction in California, the District of Columbia and Maryland, Florida, Illinois, Kentucky, Louisiana, Nebraska, New York, North Carolina, Ohio, Oregon, Puerto Rico, South Dakota, Texas, and West Virginia. Specifies total costs, estimated Federal and non-Federal costs, and funding sources and requirements. (Sec. 102) Directs the Secretary to study and, if feasible, carry out, specified projects regarding: (1) flood control in California, Florida, Illinois, Louisiana, Michigan, Missouri, New York, Oregon, Pennsylvania, Virginia, and West Virginia (sets forth the maximum amounts of Federal funds that may be allotted for specified projects in California and Nebraska); (2) bank stabilization in Pennsylvania and Tennessee; (3) navigation in Alaska, Michigan, Minnesota, Missouri, and New York; (4) shoreline protection in Connecticut, Florida, and New York; (5) snagging and sediment removal in Minnesota; (6) habitat and environmental restoration in California; and (7) channel restoration and environmental improvement in Utah. Title II: Generally Applicable Provisions - Revises: (1) cost sharing provisions of the Water Resources Development Act (the Act) of 1986 regarding dredged material disposal areas (and deletes provisions crediting non-Federal interests with the value of dredged material disposal areas provided); (2) the Act of 1974 to require any Federal agency, in the survey, planning, or design of a project involving flood protection, to consider and address in adequate detail nonstructural alternatives to prevent or reduce flood damages; and (3) Federal law regarding shore protection, including expressing congressional intent to assist projects that involve the replacement of sand on beaches and modifying the process for determining the cost- benefit ratio of a shore protection project to require that benefits provided to the local and regional economy and ecology be considered. (Sec. 202) Increases from 25 to 35 percent the non-Federal share for nonstructural and other flood control projects. Sets forth criteria and procedures relating to the ability of a non-Federal interest to pay for flood control or agricultural water supply. Requires: (1) non-Federal interests to prepare flood plain management plans designed to reduce the impacts of future flood events in project areas; and (2) the Secretary to develop guidelines for the preparation of such plans and review policies, procedures, and techniques relating to the evaluation and development of flood control measures. (Sec. 206) Authorizes the Secretary: (1) to carry out specified aquatic ecosystem restoration and protection projects; (2) in developing and carrying out a project for navigation involving the disposal of dredged material, to select a disposal method that is not the least-cost option under specified circumstances where the incremental costs are minimal and the benefits to the aquatic environment justify its selection; and (3) to undertake surveys, plans, and studies to encourage innovative and environmentally sound engineering solutions to problems of national significance. (Sec. 215) National Dam Safety Program Act of 1996 - Requires the Director of the Federal Emergency Management Agency: (1) in consultation with appropriate Federal agencies, State dam safety agencies, and a National Dam Safety Review Board (established by this section) to establish and maintain a coordinated national dam safety program; (2) to develop a dam safety improvements implementation plan; (3) at the request of a State, to provide training for State dam safety staff and inspectors; and (4) to engage in specified research activities. Authorizes the Secretary to maintain and periodically publish information on the inventory of dams. Authorizes appropriations. (Sec. 217) Directs the Secretary to enter into cooperative agreements with non-Federal sponsors of navigation projects for development of long-term management strategies for controlling sediments. Title III: Project Modifications - Provides for modifications to specified flood control, navigation, beach erosion control, hurricane damage prevention, fish and wildlife loss mitigation, shoreline protection, and other projects in Alabama, Arizona, California, Connecticut, the District of Columbia, Florida, Georgia, Illinois, Indiana, Kansas, Kentucky, Louisiana, Maryland, Michigan, Missouri, New Jersey, New York, North Carolina, North Dakota, Ohio, Oklahoma, Oregon, Pennsylvania, Puerto Rico, Rhode Island, South Carolina, Texas, Utah, Virginia, Washington, West Virginia, Wisconsin, and Wyoming. Title IV: Studies - Requires the Secretary to: (1) review Corps of Engineers capabilities regarding rural sanitation projects for rural and Native villages in Alaska; (2) credit the non-Federal share of the cost of a feasibility study on the McDowell Mountain project, Arizona, with work done by the city of Scottsdale; (3) prepare a comprehensive river basin management plan for the Santa Ynez River basin in California; (4) complete a limited reevaluation of the authorized St. Louis Harbor Project in the vicinity of the Chain of Rocks Canal, Illinois; (5) provide assistance to Springfield, Illinois, in developing an environmental impact statement for a water supply reservoir; (6) conduct studies with respect to specified water projects in Arizona, California, Illinois, Indiana, Louisiana, Michigan, Missouri, New Hampshire, New Jersey, New York, Ohio, Texas, and Virginia; and (7) conduct a study of alternative financing mechanisms for ensuring adequate funding for the infrastructure needs of small and medium ports. (Sec. 407) Amends the Act of 1990 to increase the authorization of appropriations for a study of infrastructure needs in southern California. (Sec. 427) Authorizes studies of projects in South Carolina and the Pacific region. Title V: Miscellaneous Provisions - Deauthorizes specified projects or portions of projects in Connecticut, Maine, Massachusetts, New York, Ohio, Rhode Island, and Wisconsin. (Sec. 502) Reauthorizes specified projects in Arkansas, Illinois, Michigan, Minnesota, and New Jersey. (Sec. 503) Continues the authorization of certain projects in Michigan. (Sec. 504) Provides for Federal land conveyances in California, Ohio, Oklahoma, Oregon, and Washington. (Sec. 505) Designates specified visitors centers, lakes, bridges, and locks and dams in California, Indiana, Kentucky, Louisiana, and Tennessee. (Sec. 506) Authorizes or directs the Secretary to provide assistance for: (1) specified watershed management, restoration, and development projects in Arizona, California, Georgia, Nebraska, Pennsylvania, and West Virginia; (2) Great Lakes remedial action plans; (3) testing procedures in the Great Lakes Dredged Material Testing and Evaluation Manual; (4) specified mining activity degradation abatement projects in California, Maryland, Pennsylvania, West Virginia, and Kentucky; (5) safety improvements at the Prado Dam, California; (6) demonstrating the water quality functions found in wetlands; (7) Cocheco River, New Hampshire, encroachment issues; (8) the New York City Watershed; (9) a regional water authority in northeastern Ohio; (10) the Philadelphia, Pennsylvania Water Works; (11) the Blackstone River Valley National Heritage Corridor, Rhode Island and Massachusetts; (12) non-Federal levees in Pierce County, Washington; (13) repair and rehabilitation or upgrade of dams in Ohio and Virginia; (14) wastewater treatment remediation of pollution and contaminated riverbed sediments and related activities in Jackson County, Alabama; and (15) a flood control project for Cedar Hammock (Wares Creek), Florida. (Sec. 507) Directs the Secretary to carry out: (1) programs for the removal of silt and aquatic growth in specified lakes in New York and Illinois; (2) maintenance of specified navigation channels in California, Louisiana, Mississippi, Rhode Island, Texas, and Washington; (3) beach nourishment for 50 years at specified projects in Florida and Georgia; (4) programs to control aquatic plants in Michigan and Pennsylvania; (5) specified flood control and rainfall drainage system improvements in Louisiana; (6) specified projects for the beneficial use of dredged material and specified erosion control measures in Maryland; (7) alternative methods for decontamination and disposal of contaminated dredged material at a project in Minnesota; (8) a specified bluff stabilization project in Mississippi; (9) Hudson River, New York, habitat restoration projects; (10) a study of flood control in Grand-Neosho Basin and tributaries near Pensacola Dam in Oklahoma; (11) a project to improve the hopper dredge McFarland; (12) specified projects for flood management and environmental enhancement in Tennessee; and (13) a specified water project for the Lower Mud River, West Virginia. (Sec. 511) Directs the Secretary to develop or establish: (1) a Great Lakes tributary sediment transport model; (2) a Chesapeake Bay restoration and protection pilot program; (3) an extension of the Earthquake Preparedness Center of Expertise for the central United States near the New Madrid fault; (4) a watershed management plan for Deep River Basin, Indiana; (5) a program for providing environmental assistance to non-Federal interests in Kentucky; (6) a pilot program for providing environmental assistance to non-Federal interests in Pennsylvania; and (7) a strategy for using nonstructural measures to reduce flooding, improve water quality, and create wildlife habitat in Redwood River Basin, Minnesota. (Sec. 512) Requires the Secretary to assess or evaluate: (1) Great Lakes confined disposal facilities; (2) the feasibility of an alternative to the $25 annual pass for use of water resource project recreation facilities; and (3) procedures for the approval of materials used in beach restoration and nourishment. (Sec. 514) Extends the geographic jurisdiction of the Mississippi River Commission. (Sec. 516) Directs the Secretary to: (1) promote Federal and non-Federal cooperation in providing public recreation at water resources projects; (2) work with Mississippi in managing leases in the Sardis Lake area; (3) expedite completion of the study for the Ohio River Greenway, Indiana; (4) initiate a program to increase the use of private industry hopper dredges for the construction and maintenance of Federal navigation channels, place the Federal hopper dredge Wheeler in a ready reserve status, and develop and implement procedures to ensure that private industry hopper dredge capacity is available to meet both routine and time-sensitive dredging needs; and (5) conduct a study, and develop a strategy, for using wetland restoration, soil and water conservation practices, and nonstructural measures to reduce flood damages, improve water quality, and create wildlife habitat in specified portions of the Upper Susquehanna River basin, Pennsylvania and New York. (Sec. 517) Authorizes appropriations for: (1) construction assistance for specified environmental infrastructure projects in Mississippi, New Hampshire, and Virginia; (2) a New England Division headquarters facility; (3) a Lake Superior educational facility; and (4) construction of a visitors center at Seven Points Recreation Area, Pennsylvania. (Sec. 518) Increases appropriations authorized for: (1) projects of alternative or beneficially modified habitats for fish and wildlife; (2) a quarantine facility in Broward County, Florida; and (3) the New York bight and harbor study. (Sec. 545) Directs the Secretary to increase the length of the navigation season on the Missouri River. Prohibits the Secretary from taking actions inconsistent with the existing water control policy if such action would reduce navigability by ten or more days or cause substantial increases in flood damages. Requires that any future environmental impact statement regarding Missouri River management include a cost-benefit analysis of proposed changes in the management of the river. (Sec. 546) Prohibits any county or community located at the confluence of the Missouri and Mississippi Rivers from having its participation in Federal programs affected solely due to the raising of a levee by a public levee district if such work is approved by the relevant circuit court and is limited to no greater than an elevation sufficient to contain a 20-year flood. (Sec. 548) Authorizes the Secretary to: (1) enter an agreement with the University of New Hampshire to provide technical assistance for a water treatment technology center addressing the needs of small communities; (2) construct and operate a dredged material containment facility for the Port of New York-New Jersey; (3) make capital improvements in the New York State Canal System; and (4) enter an agreement with Marshall University, West Virginia, to provide technical assistance to the Center for Environmental, Geotechnical, and Applied Sciences. (Sec. 570) Provides for the transfer of ownership, operation, maintenance, and management of the Washington Aqueduct and for interim borrowing authority to finance capital improvements at the Aqueduct. (Sec. 574) Urges the President to negotiate with Canada to eliminate tolls along, and maximize commerce through, the St. Lawrence Seaway.