PURPOSE: Section 401 of Public Law 92-500 requires that any applicant for a federal license or permit to conduct any activity which may result in any discharge into the navigable waters shall provide the federal licensing or permitting agency a water quality certification from the state. This certification will contain such conditions that ensure the proposed activity will comply with the state water quality standards and other applicable standards as required by federal law. This rule establishes the procedure and time limitations the Department of Natural Resources will follow in issuing certifications.

1. (1) Definitions. Definitions as set forth in the Missouri Clean Water Law and 10 CSR 20-2.010 shall apply to those terms when used in this rule, unless the context clearly requires otherwise.

   1. (A) “Individual federal permit,” a United States Army Corps of Engineers (USACE) authorization that is issued following a case-by-case evaluation of a specific project involving the proposed discharges in accordance with the procedures of 33 CFR part 325 and a determination that the proposed discharge is in the public interest pursuant to 33 CFR part 320. Individual federal permits will always require an individual water quality certification.

   2. (B) “Nationwide permit,” a USACE authorization that is designed to regulate with little delay or paperwork issued on a nationwide basis for a category or categories of activities when—

      1. 1. Those activities are substantially similar in nature and

cause only minimal individual and cumulative environmental impacts; or

1. 2. The nationwide permit would result in avoiding

unnecessary duplication of regulatory control exercised by another federal, state, or local agency provided it has been determined that the environmental consequences of the action are individually and cumulatively minimal in accordance with 33 CFR part 325.2(e) and 33 CFR part 330. (C) “Programatically certified” or “pre-certified,” a federal nationwide permit may be considered programmatically certified by USACE if it meets the conditions established by the department. Pre-certified nationwide permits do not need an additional department review process. This is the most stringent combination of federal permit and state water quality certification. (D) “Individual water quality certification,” individual federal permits or nationwide permits that do not meet the programmatic certification conditions. These projects require an additional review from the department to ensure that Missouri water quality standards will not be violated. (E) “Regional general permit,” a regional general permit is issued for a specific geographic area by an individual Corps District. Each regional general permit has specific terms and conditions, all of which must be met for project-specific actions to be verified.

1. (2) Requests for water quality certifications should be sent by the applicant directly to the Department of Natural Resources, Water Pollution Control Program, PO Box 176, Jefferson City, MO 65102 or by email. The request to the department should include a project narrative requesting the state’s water quality certification for the proposed project, a copy of the federal license or permit application submitted to USACE, and any readily available water quality related materials that informed the development of the federal license or permit application. If the applicant believes a project will be authorized by a general or nationwide 404 permit for which USACE has accepted the department’s programmatic certification, the applicant need not send an application to the department.

2. (3) Public Notice Procedures.

   1. (A) For individually permitted projects, USACE will issue a department/federal public notice on the permit application. This will fulfill the department’s public notice requirements and will be known as a joint public notice.
   2. (B) Projects under a nationwide permit or regional general permit that are not programmatically certified will go through the department’s public notice process. A comment period of at least fifteen (15) days will be provided. The public notice will express the department’s intent to certify the proposed project after completion of the public notice period and resolution of any adverse water quality comments received.
   3. (C) Nationwide or regional general permits that are programmatically certified are not required to go through a public notice process.

3. (4) After the completion of the public notice period, comments received shall be reviewed and considered by the department. Consideration shall be given to both direct and indirect water quality effects before issuing or denying water quality certification.

   1. (A) The department will follow public notice procedures pursuant to 10 CSR 20-6.020(4)(A).

   2. (B) If objections to the proposed project are raised during the public notice period, the department will attempt to resolve the objections.

      1. 1. If the comments are resolved during negotiations or

during public hearings, the department will proceed to issue its certification.

1. 2. If the comments are not resolved, the department shall

review the comments and proceed as follows:

1. A. 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

1. B. If the comments are determined to be invalid or not

having substantial effects upon water quality, the department shall issue its certification.

1. (5) Applications for water quality certifications have a sixty- (60-) day period in which they must be issued, waived, or denied. This period starts when a complete request is received by the department.

   1. (A) The federal agency and the department may agree in writing to extend the time to respond to a request for individual certification up to one hundred eighty (180) days if an extension is approved by the Missouri Clean Water Commission in accordance with subsection 644.051.20, RSMo, of the Missouri Clean Water Law. The commission hereby determines that extensions may be necessary to evaluate significant impacts on water quality standards if the department finds there is substantial public interest in the proposed project.
   2. (B) Submission of an incomplete request may result in the denial of water quality certification without prejudice.
   3. (C) If a water quality certification action has not been taken within sixty (60) days of the date that the complete request has been received by the department, and the department and federal agency have not agreed to extend the certification period, water quality certification will be deemed to have been waived for the activity contained in the complete request.
2. (6) Water quality certifications that are issued for nationwide and regional general permits and are programmatically certified become effective upon issuance. Water quality certifications that are issued for individual certifications and for certifications for nationwide and regional general permits that are not programmatically certified shall become effective upon signature and receipt of applicable fees. Water quality certifications are effective for the life of the federal permit.
3. (7) The issuance, conditional issuance or denial of certification under subparagraph (4)(B)2.A. or B. of this rule may be appealed to the Missouri Clean Water Commission through procedures outlined in the Revised Statutes of Missouri, Chapter 644. The appeal shall be a contested case and notice of the appeal shall be filed with the commission within thirty (30) days of service of notice to the applicant of denial or grant of the requested certification as specified in 10 CSR 20-6.020(5).
4. (8) Effective Date. This rule becomes effective immediately upon adoption and compliance with the requirements of subsection 644.036.3 of the Missouri Clean Water Law.

AUTHORITY: section 644.026, RSMo 2016.* Original rule filed Feb. 10, 1978, effective July 13, 1978. Amended: Filed May 11, 1984, effective Oct. 15, 1984. Amended: Filed Nov. 9, 2000, effective July 30, 2001. Amended: Filed July 15, 2025, effective Feb. 28, 2026. *Original authority: 644.026, RSMo 1972, amended 1973, 1987, 1993, 1995, 2000, 2012, 2014.