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 (WQC).

Any federal license or permit for an activity that may result in a discharge requires a Clean Water Act (CWA) Section 401 [33 U.S.C. 1341] Water Quality Certification (WQC) 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 CWA [33 U.S.C. 1251 et seq.] and the Missouri Clean Water Law [Chapter 644, RSMo]. The certifying authority has four action options upon request for WQC: grant, grant with conditions, waive, or deny. No federal license or permit may be granted until WQC has been obtained or waived, and no federal license or permit may be granted if WQC is denied. Virtually all Missouri WQCs are granted with conditions.

Most WQCs are for activities covered under U.S. Army Corps of Engineers (USACE) CWA 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 (IP), Nationwide Permits (NWP), and General Permits (GP). NWPs and GPs authorize activities that will result in minimal environmental impacts. IPs authorize projects that result in more than minimal environmental impacts, and each IP requires an individual WQC from the Department. Most projects are authorized under NWPs and qualify for the programmatic WQC (pre-certified). Programmatic WQCs contain a pre-established set of conditions that are applied to applicable NWPs 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 WQC, an individual WQC is required. Each GP has a specific set of pre-established conditions. Refer to those GPs for those conditions. If the project will not comply with one or more of the conditions for the specific GP, an individual WQC is required. Individual WQC for NWPs and GPs is most commonly required for projects that occur on particular impaired streams. Federal NWPs, general conditions, and definitions are available on the USACE website.

Other federal actions that may require WQC 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.

Public Notices

The applicants listed below have applied for a Section 401 WQC. According to the Missouri Clean Water Law, located in Missouri Revised Statues, Chapter 644, RSMo, and the federal Clean Water Act, proposed certifications are tentative pending public comment. Comments should be confined to the issues relating specifically to the proposed action and its effect on water quality. The department cannot consider comments or objections to a proposed certification based on issues outside the Clean Water Commission's authority (Curdt v. Mo. Clean Water Commission, 586 S.W.2d 58 Mo. App. 1979).

All comment deadlines and instructions regarding how to submit comments are stated within each public notice below. If the department receives a large number of public comments, a public meeting or public hearing may be scheduled about that proposed certification, in order for the public to ask questions, discuss issues and submit additional comments. All comments are treated with equal consideration, regardless of how they are submitted. At the end of the public comment period, the department will review and consider all comments before making a final decision regarding the proposed certification.

Notice Areas of Focus Topic Meeting/ Hearing Info
Canadian Pacific Kansas City Southern Proposed 401 Water Quality Certification Public Comment Period, Sept. 15, 2023 to Oct. 6, 2023
Water Protection Program
Water » Section 401 Water Quality Certification Proposed 401 Water Quality Certification
Section 401 Water Quality Certification
No public meeting or public hearing scheduled.

How to Apply

How to Apply

NOTE: Obtaining a WQC for USCG permits, FERC licenses, and federally issued NPDES permits will follow a different process. For details contact the Department’s general email account

All USACE Projects Start Here:

  1. 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, to help you decide which office to contact.
  2. If the project involves a federally regulated activity and permit within federally jurisdictional waters, there are two types of WQC.
    • Programmatic WQC (precertified): If the USACE issues a NWP or GP and the proposed project complies with required Missouri WQC general or specific conditions, the USACE will issue the permit with a programmatic WQC, and the project is considered precertified. Review by the Department for individual WQC is not required.
    • Individual WQC: All USACE Individual Permits require an individual WQC. If the USACE issues a NWP or GP that does not comply with one or more Missouri WQC general or specific conditions, an individual WQC is required. 
  3. If the activity is pre-certified, the USACE will notify the applicant and provide the appropriate programmatic WQC. At this point the project is certified and work may begin. No further actions are required.
  4. If an individual permit is required, follow the specific steps below for NWP/GP or an IP detailed below:
  5. Applications and additional information

More Information