Water Pollution Program Improvement Act of 2000

Water Pollution Program Improvement Act of 2000 - Requires the Administrator of the Environmental Protection Agency to make arrangements with the National Academy of Sciences (NAS) to conduct a study on the: (1) scientific basis underlying the development and implementation of total maximum daily loads for pollutants in waters for which effluent limitations under the Federal Water Pollution Control Act are not stringent enough to implement applicable water quality standards; (2) costs of implementing measures to comply with such loads; and (3) availability of alternative programs or mechanisms to reduce the discharge of pollutants from point sources and nonpoint source pollution to achieve water quality standards. Requires the NAS to report on the study to the Administrator and specified congressional committees. Provides for Federal, State, and private sector comments on such report. Authorizes appropriations.

Requires the Administrator, before making a final determination with respect to the Proposed Revisions to the National Pollutant Discharge Elimination System Program and Federal Antidegradation Policy and the Proposed Revisions to the Water Quality Planning and Management Regulations Concerning Total Maximum Daily Loads of August 1999, to: (1) review the NAS report and incorporate recommendations into the proposed revisions; and (2) publish in the Federal Register and receive public comment on incorporated recommendations and those that weren't incorporated, with an explanation why they were not incorporated. Bars the Administrator from making such final determination until the conclusion of the public notice and comment period.

Prohibits the Administrator, for purposes of ensuring that States continue to have exclusive authority to regulate nonpoint sources of pollution, from: (1) taking any action to affect any definition of, or distinction made between, point and nonpoint sources of pollution contained in an EPA rule in effect on June 1, 2000; and (2) requiring approval of any measures set forth by a State to control nonpoint sources of pollution pursuant to the Federal Water Pollution Control Act, except as authorized under specified provisions regarding nonpoint source management programs.