Start by notifying your state water quality agency that you are interested in 401 certifications in some or all of the state’s watersheds.
Many of the specific provisions for public involvement vary by state. The Clean Water Act requires that states establish procedures for public notice for all 401 certifications and public hearings for “specific applications” (CWA, Section 401(a)(1)). Thus, you must ask your state agency or look to individual state rules implementing Section 401 to determine the procedures for public notice and hearings.
Document the violations of the conditions and the water quality impacts. Submit a complaint to the federal agency that issued the permit, the state agency that issued the certification and the permittee. Send a copy of your complaint to your EPA Regional office. If there is no response, or if the response is inadequate, consider filing a 60-day notice of intent to sue. The Clean Water Act citizen suit provision gives you the right to sue the permit holder to enforce 401 conditions (CWA, Section 505(f)(5), See Lesson 9: Enforcing the Clean Water Act).
Unfortunately, this is a much trickier situation. Because the 401 certification is considered a “discretionary duty” for your state or any other certifying agency, citizens may not use the CWA to sue the certifying agency for waiving their right to make sure that all activities occurring within their jurisdiction, that require a federal license or permit, comply with water quality standards. Because states have individual regulations for implementing Section 401, there may be some states that allow for citizen appeal when a certification is intentionally or automatically waived. Otherwise, you would need to examine the provisions of the federal permit that was issued to see whether it protects water quality.