Perkins County Rural Water System Act of 1999

Perkins County Rural Water System Act of 1999 - Directs the Secretary of the Interior to make grants to the Perkins County Rural Water System, Inc. (Corporation) for the Federal share of the costs of: (1) planning and construction of the Corporation's water supply system; and (2) repairs to existing public water distribution systems to ensure conservation of resources and to make such systems functional under the new water supply system. Prohibits the obligation of water supply system construction funds until: (1) Federal environmental compliance requirements have been met; and (2) a final engineering report and plan for a water conservation program have been prepared and submitted to the Congress for at least a 90-day period.

Requires the mitigation of fish and wildlife losses during water supply system construction and operation on an acre-for-acre basis, based on ecological equivalency, and concurrent with project construction.

Directs the Western Area Power Administration to make available, from power produced under the Pick-Sloan Missouri River Basin Program, the capacity and energy required to meet the pumping and incidental operational requirements of the water supply system from May 1 to October 31 of each year. Provides power use conditions.

Provides the Federal share (75 percent) of such water supply system costs.

Authorizes the Secretary, at the Corporation's request, to provide the Corporation assistance in overseeing matters relating to water supply system construction. Limits the amount that may be used by the Secretary for planning and construction of the water supply system to three percent of the total project construction budget for the portion of the project to be constructed in Perkins County, South Dakota.

Authorizes appropriations.