To amend the Water Resources Development Act of 1986 concerning management of the upper Mississippi River system, and for other purposes.

Amends the Water Resources Development Act of 1986, with respect to management of the Upper Mississippi River system, to: (1) provide for the implementation of a combined long-term resource monitoring, computerized data inventory and analysis, and applied research program; (2) revise reporting requirements to require a report every six years beginning December 31, 2004, containing an evaluation of such program, providing updates of a systemic habitat needs assessment, and identifying any needed adjustments in the authorization; (3) extend and increase authorized appropriations; and (4) extend the authorization for the transfer of appropriated amounts between authorized programs.

Directs the Secretary of the Army to complete the on-going habitat needs assessment conducted under the Act not later than September 30, 2000, and to include in each six-year report the most recent habitat needs assessment conducted.

Permits not more than 80 percent of the non-Federal share of first costs for activities to enhance fish and wildlife resources to be satisfied through in-kind contributions, including facilities, supplies, and services that are necessary to carry out the enhancement project.