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, then the department will not issue Water Quality Certification for the project.

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.

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.

Length of Certification

This certification is valid for five years.

Laws, Rules and Regulations

How to Apply

NOTE: Obtaining a Water Quality Certification for USCG permits, FERC licenses, and federally issued NPDES permits will follow a different process. For details contact the department’s water quality certification general email account.

All USACE Projects Start Here:

  • If you are considering a project that may involve placing fill material in a lake, river, stream, dry streambed, or wetland, you should contact the USACE to determine if the project you are planning is within federally jurisdictional waters and is a regulated activity that requires a federal permit. If no federal permit is required, no state WQC is required. Refer to the USACE District map, which includes contact numbers and email addresses, to help you decide which office to contact.
  • If the project involves a federally regulated activity and permit within federally jurisdictional waters, there are two types of Water Quality Certification.
    • Programmatic Water Quality Certification (precertified): If the USACE issues a Nationwide or General permit and the proposed project complies with required Missouri Water Quality Certification general or specific conditions, the USACE will issue the permit with a programmatic Water Quality Certification, and the project is considered precertified. Review by the department for individual Water Quality Certification is not required.
    • Individual Water Quality Certification: All USACE Individual Permits require an individual Water Quality Certification. If the USACE issues a Nationwide or General permit that does not comply with one or more Missouri Water Quality Certification general or specific conditions, an individual Water Quality Certification is required. 
  • If the activity is pre-certified, the USACE will notify the applicant and provide the appropriate programmatic Water Quality Certification. At this point the project is certified and work may begin. No further actions are required.
  • If an individual water quality certification permit is required, follow the specific steps below for a Nationwide or General permit or an Individual Permit detailed in the fact sheets listed below
  • Applications and additional information listed below.

Applications

Fact Sheets

Fees

  • $150 for a 401 Certification project that requires a Finding of No Significant Impact but does not require an Environmental Impact Statement
  • $1,500 for a 401 Certification project that does require an Environmental Impact Statement. 

Timeline/ Process

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, then the department will not issue Water Quality Certification for the project.

The department has a 60-day period to issue or deny a complete requests for water quality certifications. This period starts when a complete application is received by the department. Applications for water quality certification for activities requiring individually certified nationwide permits also have a 60-day period to be issued or denied by the department. Either of these periods may be extended by mutual agreement of the applicant and the department. Submission of an incomplete application does not start the 60-day timeline. 

NOTE: Additional details regarding the timeline and process are included in the “How to Apply” tab.

Public Participation

Individual Water Quality Certification for Nationwide or General permits

The draft Water Quality Certification will be placed on public notice for 21 days. If substantive comments are received, the department will respond and, if necessary, the Water Quality Certification will be updated. Substantive changes to the draft Water Quality Certification may required another public notice and an extension of the reasonable period of time. After the department’s public notice, the Water Quality Certification will go through a final review and approval process.

USACE Individual Permits

In order to minimize delay in construction for individually permitted projects, the USACE issues a MoDNR/federal public notice on the permit application. A reasonable comment period, normally 30 days, but not fewer than 15 days is provided. Individual public notices are not used for projects authorized by general or nationwide permits.

The joint public notice will express MoDNR’s intent to certify the proposed project after completion of the public notice period and resolution of any adverse water quality comments received. The USACE will forward public comments to the department for review and consideration. The department will consider comments related to direct and indirect water quality effects before issuing or denying water quality certification. Direct effect comments pertain to a water quality problem that would result from the actual work on the proposed project such as increased turbidity, improper disposal of dredge and fill material and siltation. Indirect effects include long or short range effects that are likely to occur as a result of the proposed construction but are not anticipated to cause water quality problems or pollution at the time of initial construction activity.

If no objections are received during the public notice period and the department determines that no adverse water quality problems are reasonably anticipated, the department will issue a certification with provisions that if adverse water quality problems develop during construction the certification may be suspended pending resolution of the problem(s). If objections to the proposed project are raised during the public notice period, the USACE and MoDNR will attempt to resolve the objections. If sufficient public interest is expressed, a public hearing will be held.  If the comments are resolved during negotiations or during public hearings conducted by the federal agency, the department will proceed to issue its certification. If the comments are not resolved, the department proceed as follows: 

  • If the comments are determined to be valid comments, the department shall either deny certification or issue a certification that is conditioned upon the applicant meeting certain requirements or performing certain actions to prevent or minimize water quality problems; or 
  • If the comments are determined to be invalid or not having substantial effects upon water quality, the department shall issue its certification.

Administrative Hearing Commission

Anyone who is adversely affected by the director's decision to issue, deny, suspend or revoke a permit must appeal within 30 days of the decision to the Administrative Hearing Commission as provided by 621.250.3 RSMo. All appeals must be filed by petition and send to:

Administrative Hearing Commission
PO Box 1557
Jefferson City, MO 65102
Phone: 573-751-2422
Fax: 573-751-5018
Website: Administrative Hearing Commission

Requirements

The following requirements must be met in order to have a complete request for Water Quality Certification (WQC).

  • A complete request for WQC [10 CSR 20-6.060(5) and 40 CFR 121.5] ensures sufficient information necessary for the department to draft a WQC and ensure compliance with Missouri water quality requirements. The regulatory clock starts with a complete request for WQC. Documentation should match the complexity of the project.
  • Complete WQC Request Requirements, Federal [40 CFR 121.5(a)(1)]:
    • A copy of the federal permit application submitted to the federal agency.  
    • Provide any readily available water quality-related materials that informed the development of the application.
  • Complete WQC Request Requirements, State [10 CSR 20-6.060(5)]:
    • USACE Application
    • Topographical Maps
    • Location Maps
    • Engineering Plans
    • Project Diagrams
    • Compensatory Mitigation Plans (where applicable)
      1. Missouri Stream Mitigation Method Adverse Impact Worksheets
      2. Name of Mitigation Bank or In-Lieu Fee Provider
      3. Location of Mitigation Site
      4. Permittee-Responsible: Permittee-Responsible mitigation plans should be reviewed and approved by the department prior to certification request, and must satisfy the 12 elements of a mitigation plan defined in the 2008 Mitigation Rule.
  • General Information Needed (should be contained in documents above):
    • Project activity (bank stabilization, bridge replacement, residential housing, etc.)
    • Type of Aquatic Resource (stream name/type, wetland type, etc.)
    • Extent of Impacts (linear ft of stream, acres of wetland, etc.)
    • Equipment or measures planned to treat, control, or manage discharge

Reporting

There are no reporting requirements on behalf of the Missouri Department of Natural Resources for general 401 certifications. The U.S. Army Corps of Engineers maintains jurisdiction for reporting requirements.

Renewal

Water Quality 401 Certifications are effective for the life of the 404 Compensatory Mitigation permit. The U.S. Army Corps of Engineers requires regular recertification (typically every five years) for long-term projects, such as dredging. These are completed on request of the Corps and permitted entity.

Resources

U.S. Army Corps of Engineers Useful Links

Missouri USACE’s Districts Map and Contacts 

Compensatory Mitigation

MoDNR Supporting Documents

Other Federal Permits that May Result in a Discharge

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