Section 401 Water Quality Certification

Important: Prior to performing any work in a waterway or wetland, contact the appropriate U.S. Army Corps of Engineers (USACE) district to determine if a federal permit is required. If there is no federal permit, there is no Water Quality Certification.

Any federal license or permit for an activity that may result in a discharge requires a Clean Water Act Section 401 [33 U.S.C. 1341] Water Quality Certification from the state certifying authority, the Missouri Department of Natural Resources (the department). This ensures that federally authorized projects will comply with applicable provisions of the Clean Water Act [33 U.S.C. 1251 et seq.] and Missouri Clean Water Law [Chapter 644, RSMo]. The certifying authority has four action options upon request for Water Quality Certification: grant, grant with conditions, waive, or deny. No federal license or permit may be granted until certification has been obtained or waived, and no federal license or permit may be granted if WQC is denied. Virtually all Missouri Water Quality Certifications are granted with conditions.

Most Water Quality Certifications are for activities covered under U.S. Army Corps of Engineers (USACE) Clean Water Act Section 404 permits authorizing the placement of dredge or fill material into jurisdictional waters, also known as waters of the U.S. Waters of the U.S. are rivers, streams (wet and dry), lakes, and wetlands; and jurisdictional determinations are made by the USACE. Common activities include stream bank stabilization, installation or replacement of culverts and low water crossings, fill impacts related to residential and commercial developments, and infrastructure maintenance. To learn more about the 404 permits visit the USACE’s Regulatory Program and Permits website. 

The USACE authorizes projects with Individual Permits, Nationwide Permits and General Permits. Nationwide and General permits authorize activities that will result in minimal environmental impacts. Individual Permits authorize projects that result in more than minimal environmental impacts, and each Individual Permit requires an individual Water Quality Certification from the department. Most projects are authorized under Nationwide Permits and qualify for the programmatic Water Quality Certification (pre-certified). Programmatic Water Quality Certifications contain a pre-established set of conditions that are applied to applicable Nationwide Permits and are provided by the USACE upon issuance of a permit. If the project will not comply with one or more of the conditions of the programmatic Water Quality Certification, an individual Water Quality Certification is required. Each General Permit has a specific set of pre-established conditions. Refer to those General Permits for those conditions. If the project will not comply with one or more of the conditions for the specific General Permits, an individual Water Quality Certification is required. Individual Water Quality Certification for Nationwide Permits and General Permits is most commonly required for projects that occur on particular impaired streams. Federal Nationwide Permits, general conditions and definitions are available on the USACE website.

• Programmatic Clean Water Section 401 Water Quality Certification for Nationwide Permits: 2020 General and Specific Conditions (Nationwide Permits - 12, 21, 29, 39, 40, 42, 43, 44, 48, 50, 51, 52, 55, 56, 57 and 58)

• Programmatic Clean Water Section 401 Water Quality Certification for Nationwide Permits 2021 General and Specific Conditions (Nationwide Permits - 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 25, 27, 30, 31, 32, 33, 34, 36, 37, 38, 41, 45, 46, 49, 53, 54 and 59)

Other federal actions that may require Water Quality Certification include U.S. Coast Guard (USCG) permits, Federal Energy Regulatory Commission (FERC) licenses, and federally issued National Pollutant Discharge Elimination System (NPDES) permits, but these permits and licenses are much less common.