Clean Water Enforcement and Compliance Improvement Act of 2003

Clean Water Enforcement and Compliance Improvement Act of 2003- Amends enforcement provisions of the Federal Water Pollution Control Act (FWPCA) regarding: (1) findings concerning harm caused and citizen suits; (2) compliance under State permits; (3) recordkeeping, effluent monitoring, and notice of pollution information; (4) priority areas (with a high degree of economic distress or social disenfranchisement); (5) violations of pretreatment requirements; (6) amounts of penalties; (7) the effect of State actions upon Federal ones; (8) inspection of significantly noncomplying facilities; and (9) the scope of Environmental Protection Agency (EPA) emergency powers.

Revises State pollutant discharge permit program requirements concerning program approval, inspection, monitoring, introduction of pollutants into publicly owned treatment works, poor compliance histories, submission of pollution prevention plans, and reporting.

Restricts the duration of permits that modify effluent limitations for toxic pollutants to two years and requires a hearing concerning owner-operator control and reasonable progress.

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

Includes in employee protections a prohibition against harassment or prosecution of, or discrimination against, persons for assisting in achieving compliance with, or refusing to violate, FWPCA.

Expands EPA subpoena authority and subjects additional actions under FWPCA to judicial review.

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.