A state may deny certification altogether if it believes that a project will cause or contribute to a violation of its water quality standards. For example, the Oregon Department of Environmental Quality denied the City of Klamath Falls' application for certification of a new hydroelectric project on the Klamath River because models showed the river would not meet state water quality standards for temperature if the project went forward.
States are often required to review general permits that cover entire categories of activity. Once 401 certification is granted to a general permit, the certification applies to all entities whose activities are subsequently covered by the general permit. States can deny or condition 401 certification for a general permit (thus an entire category of activity) but not for each activity covered by the general permit.
Any conditions imposed by a state as part of the 401 certification process become conditions of the federal permit. Instream flow requirements found in most certifications for relicensing hydropower dams require continuous monitoring and evaluation. Section 401 requires that certifications include “monitoring requirements necessary to assure that any applicant for a Federal license or permit will comply with” applicable limitations, including state water quality standards (CWA, Section 401(d)).
Either the state agency or the federal agency issuing the license or permit can enforce the conditions of 401 certification. The 401 conditions are also enforceable by citizen suits (CWA, Section 505(f)(5)). For example, if Tacoma City Light does not maintain the instream flows ordered by the State of Washington in PUD No.1 of Jefferson County v. Washington Department of Ecology, private citizens can sue the utility to force compliance with those conditions.
A state certification is required to have several elements including “reasonable assurance” that water quality standards will be met (40CFR121.2(a)(3)). Therefore, if a state certifies a federal permit despite evidence that the permit will violate water quality standards, citizens can sue in state court to add or improve the conditions or to have the certification revoked. Thus, citizens can stop the activity (because the permit is not valid without the certification) until the applicant provides reasonable assurance that the facility or activity will not violate water quality standards.