Clean Water Enforcement and Compliance Improvement Act of 2000

Provides for the imposition of penalties for violations of pretreatment program requirements.

Removes provisions that permit State enforcement actions to serve as a bar to Federal enforcement actions.

Directs the Administrator of the Environmental Protection Agency to: (1) conduct inspections of facilities operated by significant noncompliers at which violations occurred; and (2) report annually to Congress and State Governors on significant noncompliers.

Requires State pollutant discharge permit programs to include specified inspection, monitoring, and reporting requirements.

Prohibits the issuance of permits to significant noncompliers until conditions giving rise to violations have been corrected.

Requires discharge permit applicants to submit pollution prevention plans to the Administrator.

Authorizes citizen suits for past violations of effluent standards or limitations if there is evidence that violations have been repeated.

Amends employee protection provisions of the Act, to include a prohibition against harassment or prosecution of, or discrimination against, persons for assisting in achieving compliance with, or refusing to violate, the Act.

Establishes the Clean Water Trust Fund for mitigation projects.

Makes Federal agencies subject to all Federal, State, and local water pollution control and abatement requirements in the same manner as any other person. Waives sovereign immunity of the United States with respect to such requirements.