Water Protection Program fact sheet
Division of Environmental Quality Director: Kyra Moore
PUB3028

Consistent with Section 401 of the Clean Water Act (CWA) [33 U.S.C. § 1341] and the Missouri Clean Water Law [Chapter 644, RSMo], below are the steps for obtaining an individual Water Quality Certification (WQC)
from the Missouri Department of Natural Resources (Department) for U.S. Army Corps of Engineers (USACE) Nationwide Permits (NWPs) and General Permits (GPs).

Individual WQC for Nationwide Permits and General Permits:

  1. Pre-filing Meeting Request: Per the federal 2020 Certification Rule, the project proponent must request a pre-filing meeting at least 30 days prior to requesting a WQC from the Department [40 CFR§121.4(a)]. Pre-filing meeting requests should be sent directly to the Department’s general email account. The Rule allows no flexibility on shortening the 30 day timeframe; contact the Department immediately to address emergency situations. Depending on the proposed project, the Department may or may not require a meeting and will respond accordingly.
    • Encouraged to Discuss: The project proponent and the certifying authority are encouraged to discuss the nature of the proposed project and potential water quality effects. The project proponent is encouraged to provide a list of other required state, interstate, tribal, territorial and federal authorizations and to describe the anticipated timeline for construction and operation. [40CFR §121.4(c)].
    • Other Topics of Discussion: The project proponent and certifying authority may also discuss additional information needed to sufficiently ensure compliance with the Missouri Clean Water Law [Chapter 644, RSMo], such as potential NPDES permitting, receiving stream conditions, compensatory wetland and/or stream mitigation information, and the timing of WQC request to avoid deadline issues and potential denial of WQC.
  2. Complete WQC Request: Once the applicant has finalized project plans, knows what permit the USACE will use, and has waited at least 30 days from the pre-filing meeting request, the WQC may be requested. WQC requests should be sent to the Department’s general WQC email account. Per the federal 2020 Certification Rule, the following requirements must be met in order to have a complete request for WQC.
    • WQC request shall be submitted to the certifying authority and to the federal agency concurrently [40 CFR §121.5(a)].
    • WQC request shall [40 CFR §121.5(b)(1-9)]:
      1. Identify the project proponent(s) and a point of contact
      2. Identify the proposed project
      3. Identify the applicable federal license or permit
      4. Identify the location and nature of any potential discharge that may result from the proposed project and the location of receiving waters
      5. Include a description of any methods and means proposed to monitor the discharge and the equipment or measures planned to treat, control, or manage the discharge
      6. Include a list of all other federal, interstate, trial, state, territorial, or local agency authorizations required for the proposed project, including all approvals or denials already received
      7. Include documentation that a pre-filing request was submitted to the certifying authority at least 30 days prior to submitting the certification request
      8. Contain the following statement: ‘The project proponent hereby certifies that all information contained herein is true, accurate, and complete to the bet of my knowledge and belief
      9. Contain the following statement: ‘The project proponent hereby requests that the certifying authority review and take action on this CWA 401 certification request within the applicable reasonable period of time.’
  3. Reasonable Period of Time: The WQC clock starts once a request that contains all of the above information is received by the Department. The federal agency will establish the Reasonable Period of Time (RPT) in which the certifying authority may act on a WQC request. This is typically 60 days from the date of the request, and it shall not exceed one year [33 U.S.C. §1341(a)(1)]. The federal agency may extend the RPT at the request of a certifying authority and/or a project proponent [40 CFR §121.6(d)].
  4. Sufficient Information to Certify: The Department will review the WQC request and determine if there is sufficient information needed to certify the project will comply with Missouri water quality requirements. If the request is determined insufficient, the Department will request further information necessary to draft the WQC and ensure the discharge will comply with water quality requirements [40 CFR §121.7(b)]. Submitting insufficient information or failing or refusing to provide additional information upon request may result in the denial of WQC if the state cannot certify that the discharge will comply with water quality requirements [40 CFR §121.7(b)]. If the certifying authority issues a denial of WQC, the project proponent may resubmit a new WQC request [40 CFR §121.8(a)]
    • Sufficient Information for WQC: Upon request for WQC, the project proponent should provide sufficient information necessary for the Department to draft a WQC and ensure compliance with Missouri water quality requirements. Documentation should match the complexity of the project. Sufficient information includes documents specified in 10 CSR 20-6.060(5):
      • USACE Application
      • Topographical Maps
      • Location Maps
      • Engineering Plans
      • Project Diagrams
      • Compensatory Mitigation Plans (where applicable)
    • General Information Needed (may 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
  5. Draft WQC: Once the Department receives sufficient information about the proposed project and its discharge, the WQC will be drafted, reviewed, and, if appropriate, approved by the Water Protection Program.
  6. MoDNR Public Notice: The draft WQC will then be placed on Public Notice, typically for 21 days. If substantive comments are received, they will be responded to, and, if necessary, the WQC will be updated. Substantive changes to the draft WQC may require another Public Notice and an extension of the RPT.
  7. Issue WQC: After the Department Public Notice, the WQC will go through a final review and approval process. If approved by the Water Protection Program, the final WQC will be issued and emailed to the applicant and the federal agency. WQC conditions become part of the federal permit [33 U.S.C. §1341(d)], and the federal agency is responsible for enforcing WQC conditions [40 CFR §121.11(c)].
  8. Pay Fee and Effective: The WQC becomes effective upon receipt of the fee specified in the WQC [10 CSR 20-6.060(6)]. It remains effective until the federal permit is expired or terminated. If a fee is not received, the WQC is not effective and the project is not certified. There are two fee types for individual WQCs [10 CSR 20-6.011(H)].
    • Fee: $150 - Projects do not require an Environmental Impact Statement or an Environmental Impact Statement resulted in a Finding of No Significant Impact
    • Fee: $1,500 - Projects that did require an Environmental Impact Statement that did not result in a Finding of No Significant Impact
  9. Modifications: Although previously allowed, modifications are not authorized by the federal 2020 Certification Rule [40 CFR Part 121]. WQCs are for plans as submitted, reviewed, and certified in compliance with the procedures defined in the 2020 Certification Rule. Any project plans omitted from the request for WQC or any future project expansions or modifications must obtain a new WQC in compliance with the 2020 Certification Rule.
  10. Appeal: WQCs (or denials) may be appealed to the Missouri Clean Water Commission [10 CSR 20-6.060(7)]. Appeals must be filed within 30 days of issuance to the Administrative Hearing Commission (AHC) [Section 621.250, RSMo].

For more information

Missouri Department of Natural Resources
Water Protection Program
PO Box 176
Jefferson City, MO 65102-0176
wpsc401cert@dnr.mo.gov
800-361-4827 or 573-522-4502
Section 401 Water Quality Certification


Nothing in this document may be used to implement any enforcement action or levy any penalty unless promulgated by rule under chapter 536 or authorized by statute.


For more information