Section 401 of the federal Clean Water Act (33 USC 1341) grants direct authority to each state to issue a Water Quality Certification for any project requiring a federal permit or license. This certification authority is provided for the state to verify that a federally authorized project does not violate state water quality requirements. To help project proponents avoid and minimize impacts to water quality, the department may require conditions on projects as part of a water quality certification.

Although water quality certifications are issued in association with federal licenses, such as Federal Energy Regulatory Commission hydropower licenses, most water quality certifications are issued for U.S. Army Corps of Engineers’ (USACE) Clean Water Act Section 404 Department of Army Permits, known as 404 permits. These permits authorize placing material or fill into the jurisdictional waters of the United States. Examples of placing fill include, but are not limited to, riprap along stream banks, culverts under road crossings, armoring for stormwater outfall pipes and general fill for residential and commercial developments. The term jurisdictional waters refers to lakes, rivers, streams and wetlands, including those that do not always contain water. Jurisdictional determinations are made by the USACE. For more information about the 404 Permit and water quality certification process, visit the USACE’s Regulatory Program and Permits website.

The USACE authorizes projects for both individual and general 404 permits. All individual 404 permits require department review for individual water quality certification. The USACE often issues a general permit subject to a set of general, pre-established conditions, to expedite issuing a large number of 404 Permits to authorize activities that have minimal individual and cumulative adverse environmental effects. A USACE nationwide permit is a common general permit available across the United States (with some exceptions) to authorize a variety of common project types, such as streambank stabilization, utility crossings, outfall structures and residential or commercial development. Federal nationwide permits, general conditions, and definitions can found on the USACE’s website. Most general 404 permits are pre-approved by the department, but general 404 permits not meeting general or specific conditions or occurring on particular impaired streams require individual review for certification. Missouri’s water quality certification general and specific conditions apply to nationwide permits. Other USACE general permits contain specific Missouri water quality certification general and specific conditions. Please refer to those USACE general permits for those conditions.

How to Apply

  1. If you are considering a project that may involve placing materials 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. 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 within federally jurisdictional waters, there are two types of water quality certification.
    • Programmatic Water Quality Certification: 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 certification, and review by the department for individual water quality certification is not required.
    • Individual Water Quality Certification: If the proposed project requires an individual 404 permit or does not comply with one or more Missouri water quality certification general or specific conditions, review by the department for individual certification will be required.
  3. When individual water quality certification is required, the federal Clean Water Act Section 401 Certification Rule promulgated by the U.S. Environmental Protection Agency will apply. The rule specifies how a request must be made.
  4. According to section §121.4 of the rule, you must submit a pre-filing meeting request to the department at least 30 days before requesting water quality certification. The pre-filing meeting request should be sent to the department by email to If you are not able to correspond with the department through email, please call 573-522-4502 for other options. Although the department is not required to respond to a pre-filing meeting request, the department typically responds within 14 days. The department will use this as an opportunity to discuss the 404 or 401 process with you and share potential requirements for individual water quality certification.
  5. Once the minimum 30 days has passed after submitting the pre-filing meeting request, project proponents can send a request for certification to If you are not able to correspond with the department through email, please call 573-522-4502 for other options. Federal requirements for requesting certification can be found in section §121.5 of the rule. If all requirements are not met, the department will notify the project proponent with the need to submit additional information. Once the department receives a water quality certification request that meets all requirements of the rule, the department will coordinate with you and the federal licensing or permitting agency. Within the reasonable amount of time established by the federal licensing or permitting agency, typically 60 days for 404 permits, the department will determine if it will issue, issue with conditions, deny or waive water quality certification.
  6. The department will draft its water quality certification decision and make the draft decision available for public review and comment for at least 21 days.
  7. After the close of the public comment period, the department will review all written comments, change the water quality certification according to the comments received, if necessary, and issue a final decision within the designated reasonable time period.  
  8. After the department issues a water quality certification for your project, you will receive the 401 water quality certification decision letter and an invoice for the appropriate fee according to 10 CSR 20-6.011(2)(I). The invoice contains information about how to make a payment. Please do not send a check or pay by credit card until the invoice is sent to you. When the department receives the fee, the department will notify the appropriate USACE office to notify them the certification is now final and in effect.

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
South River Industrial Levee Subdistrict Proposed Section 401 Water Quality Certification Public Comment Period, May 2, 2022 to May 23, 2022
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.

More Information

For more information about when a 404 permit is required or other questions on 404 permits, contact the USACE district office for your area as indicated on the district map, or go to the USACE Regulatory Branch website. 

Information regarding 404 Permits/ WQCs in wetlands is available in the department's Section 401 Water Quality Certification: Protecting Missouri's Wetlands - PUB2151 fact sheet. 

For more information about WQCs, contact the department by telephone at 573-522-4502 or by email at