TABLE OF CONTENTS: Title I: Water Resources Development Title II: Cheyenne River Sioux Tribe, Lower Brule Sioux Tribe, and State of South Dakota Terrestrial Wildlife Habitat Restoration Water Resources Development Act of 1998 - Title I: Water Resources Development - Authorizes projects for flood damage reduction, flood control, aquifer storage and recovery, and navigation in California, Florida, Maryland and Virginia, Minnesota, and North Dakota. Authorizes projects for water resources development and conservation and related purposes, subject to a final report from the Army Chief of Engineers and approval by the Secretary of the Army, in California, Delaware, Florida, Georgia, Minnesota, Mississippi, Missouri and Kansas, and New Jersey. (Sec. 103) Modifies projects for flood control, navigation, water conveyance, water supply storage reallocation, flood mitigation, and beach erosion control and hurricane protection (together with certain report requirements, in some cases) in Arkansas, California, Maryland, Nebraska, Nevada, New Jersey, Oklahoma, South Dakota, Virginia, and West Virginia. (Sec. 104) Deauthorizes navigation projects in Connecticut and Maine. (Sec. 105) Directs the Secretary to review reports or conduct studies with respect to specified projects in Alabama, Alabama and Florida, California, Florida, Louisiana, Mississippi, Missouri, Montana, Nevada, New Jersey, New York, South Dakota, and Washington. (Sec. 106) Authorizes the Secretary to undertake a program to reduce flood hazards and restore the natural functions and values of riverine ecosystems throughout the United States. Directs the Secretary to carry out appropriate studies in connection with the program. Requires non-Federal interests to pay 35 percent of the cost of any project carried out. Outlines project selection, policies, and criteria. Prohibits any project from being carried out until the Secretary notifies specified congressional committees and 21 days have passed since such notification. (Sec. 107) Amends the Water Resources Development Act of 1986 to provide that the non-Federal share of the costs of periodic nourishment of projects or measures for shore protection or beach erosion control shall be 50 percent, with specified exceptions. (Sec. 108) Amends the Flood Control Act of 1948 to increase to $7 million the maximum amount for small flood control projects. (Sec. 109) Amends the Flood Control Act of 1960 to authorize the Secretary to accept funds voluntarily contributed to expand the compilation and dissemination of information on floods and flood damage. (Sec. 110) Amends the Water Resources Development Act of 1996 to: (1) extend through FY 2000 the Everglades and South Florida ecosystem restoration program; and (2) allow non-profit entities to enter into agreements to pay non-Federal shares of aquatic ecosystem restoration projects. (Sec. 112) Amends the Water Resources Development Act of 1992 to allow non-profit entities to enter into agreements to pay non-Federal shares of the costs of projects for beneficial uses of dredged material. (Sec. 113) Amends the Flood Control Act of 1936 to allow contributions by States and political subdivisions to be used for environmental restoration activities. (Sec. 114) Authorizes the Secretary during FY 1999 through 2000 to withhold a specified amount of recreation user fees for repair and maintenance projects, interpretation, signage, habitat or facility enhancement, resource preservation, annual operation, maintenance, and law enforcement related to public use at recreation sites. (Sec. 115) Amends the Water Resources Development Act of 1986 to permit studies undertaken by the Secretary concerning the Pacific region to include flood damage reduction and environmental restoration. (Sec. 116) Directs the Secretary to develop a plan for a project to protect and enhance fish and wildlife habitat of the Missouri River and the middle Mississippi River. Prohibits such plan or project from affecting water rights or private property rights. Permits the modification of previously authorized projects in such areas. Requires a 35 percent non-Federal cost share. Authorizes appropriations for FY 2000 and 2001. (Sec. 117) Amends the Outer Continental Shelf Lands Act to prohibit fees from being charged to non-Federal interests for an assessment of the value of the resources and the public interest served in promoting development of Outer Continental Shelf resources. Requires full reimbursement of amounts paid by the non-Federal sponsor for beach erosion control and hurricane protection at Sandbridge Beach in Virginia Beach, Virginia, as a result of such an assessment. (Sec. 118) Amends the Water Resources Development Act of 1990 to: (1) include Snake Creek in Bixby, Oklahoma, as a priority work for environmental dredging activities; and (2) direct the Secretary to include primary flood damages avoided within a benefit analysis for justifying Federal non-structural flood damage reduction projects. (Sec. 120) Amends the River and Harbor Act of 1958 to include within projects for the control of aquatic growth projects for the control of Arundo dona and tarmarix. (Sec. 121) Amends the Water Resources Development Act of: (1) 1992 to include three water systems and projects in California and Nevada among authorized environmental infrastructure projects; (2) 1996 to include certain California and Nevada watersheds and river basins within authorized watershed management, restoration, and development; and (3) 1986 to include projects in Lake County, California, and Milford, New Hampshire, under a lakes silt and debris removal program. (Sec. 124) Authorizes the Secretary to acquire for Rhode Island a dredge and associated equipment for dredging salt ponds. (Sec. 125) Amends the Water Resources Development Act of 1996 to: (1) include the Chemung River watershed, New York, under a water resources development program for the Upper Susquehanna River Basin in Pennsylvania and New York; (2) include certain projects in New Jersey and Pennsylvania under authorized small flood control projects; and (3) include a project in Delaware Bay, New Jersey, under authorized small navigation projects. (Sec. 128) Makes the streambank protection project at Coulson Park in Billings, Montana, eligible for assistance under the Flood Control Act of 1946. (Sec. 129) Authorizes the Secretary to conduct measures to address water quality, flows, and fish habitat restoration in the historic Springfield, Oregon, millrace through reconfiguration of the existing millpond if it is determined that harmful impacts have occurred as the result of a previously constructed flood control project. Authorizes appropriations. (Sec. 130) Directs the Secretary to expeditiously complete certain previously authorized saltmarsh restoration activities in Sluice Creek, Guilford, Connecticut, and Lighthouse Point Park in New Haven, Connecticut. (Sec. 131) Designates the project for flood control, Eight Mile Creek, Paragould, Arkansas, as the Francis Bland, Arkansas Floodway Ditch No. 5. (Sec. 132) Directs the Secretary to restore breakwater integrity at Point Judith, Rhode Island, as authorized under prior law. Specifies estimated Federal and non-Federal costs. (Sec. 134) Modifies the project for flood control and other purposes at Cumberland, Maryland, to authorize the Secretary to undertake restoration of the historic Chesapeake and Ohio Canal. Specifies estimated Federal and non-Federal costs. (Sec. 135) Amends the Water Resources Development Act of 1992 to: (1) add an additional project purpose to a water resource development project in the New York-New Jersey Harbor; and (2) increase the authorization of appropriations for such project. (Sec. 136) Includes Miami Beach, Florida, under a previously authorized national shoreline erosion control development and demonstration program. Increases the authorization of appropriations for small storm damage reduction projects. (Sec. 138) Directs the Secretary to accept from Oklahoma an amount to be determined as prepayment for water supply cost obligations for water supply storage at Sardis Reservoir in Oklahoma. (Sec. 139) Directs the Secretary to proceed immediately to prepare engineering design, plans, and specifications to extend certain locks on the Mississippi and Illinois Rivers to provide lock chambers of specified dimension so that construction can proceed immediately upon completion of studies and authorization of projects by the Congress. (Sec. 140) Amends the Water Resources Development Act of: (1) 1976 to reduce from 50 to 35 the percent of total cost to be borne by States for placing dredged sand on State beaches; and (2) 1986 to state that not more than 80 percent of the non-Federal share of fish and wildlife mitigation costs may be in-kind. (Sec. 142) Amends the Water Resources Development Act of 1986 relating to the Upper Mississippi River system to: (1) add certain activities under a master plan for the improvement of the system; (2) direct the Secretary to create an independent technical review committee to review system projects, monitoring plans, and natural resources blueprints; (3) require promotion of the simulation of natural river processes to the maximum extent practicable; (4) authorize appropriations for FY 1999 through 2009 for system programs; (5) require an evaluation report from the Secretary to the Congress; (6) authorize the transfer of appropriated amounts between various programs; and (7) direct the Secretary to investigate, and if appropriate, carry out restoration of urban wildlife habitat, with a special emphasis on the establishment of greenways, in the St. Louis, Missouri, area and surrounding communities. (Sec. 144) Amends the Water Resources Development Act of 1996 relating to a research and development program for Columbia River basin salmon survival to: (1) include the Snake River in such program; (2) revise, generally, authorized activities under the program; (3) increase the authorization of appropriations for the development and installation in Corps dams of advanced hydropower turbines; and (4) direct the Secretary to carry out methods to reduce nesting populations of avian predators on dredge spoil islands in the Columbia River under the Secretary's jurisdiction (authorizes appropriations). Title II: Cheyenne River Sioux Tribe, Lower Brule Sioux Tribe, and State of South Dakota Terrestrial Wildlife Habitat Restoration - Directs the State of South Dakota, the Cheyenne River Sioux Tribe, and the Lower Brule Sioux Tribe to each develop a plan for the restoration of terrestrial wildlife habitat loss that occurred as a result of flooding related to the Big Bend and Oahe projects carried out under the Pick-Sloan Missouri River Basin program. Requires each plan to be submitted to the Secretary for review and submission to specified congressional committees. Provides funding for such plans and transitional provisions. Authorizes South Dakota to use available funds to develop a program for the purchase of wildlife habitat leases and requires such leases to provide for public access for sportsmen during hunting season and for other outdoor uses covered under the lease. (Sec. 203) Establishes in the Treasury the South Dakota Terrestrial Wildlife Habitat Restoration Trust Fund, the Cheyenne River Sioux Tribe Terrestrial Wildlife Restoration Trust Fund, and Lower Brule Sioux Tribe Terrestrial Wildlife Habitat Restoration Fund, to be used to implement wildlife habitat restoration plans authorized under this title. (Sec. 205) Directs the Secretary to transfer to the South Dakota Department of Game, Fish, and Parks specified Federal lands for fish and wildlife purposes, or public recreation purposes, in perpetuity. (Sec. 206) Directs the Secretary to transfer to the Secretary of the Interior certain Federal recreation areas, to be held in trust for the Cheyenne and Lower Brule Tribes for authorized project purposes. (Sec. 208) Authorizes appropriations to: (1) the Secretary for administrative expenses and the implementation of terrestrial wildlife habitat restoration plans; and (2) the Secretary of the Interior for administrative expenses in carrying out this title.