How to Obtain an Individual Water Quality Certification for Nationwide Permits and General Permits - PUB3028

Consistent with Section 401 of the Clean Water Act (CWA), found in U.S. Code 33 U.S.C. §11341, 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 for U.S. Army Corps of Engineers (USACE) Nationwide Permits and General Permits.

Individual WQC for Nationwide Permits and General Permits:

1. Pre-filing Meeting Request: Per the federal 2023 Certification Rule, the project proponent must request a pre-filing meeting at least 30 days before requesting a WQC from the department [40 CFR §121.4]. Pre-filing meeting requests should be sent directly to the department’s WQC general email account at wpsc401cert@dnr.mo.gov. Depending on the proposed project, the department may or may not require a meeting and will respond accordingly. If there is sufficient information to certify, the department may waive or shorten the 30-day requirement for a pre-filing meeting request.
   • Information to Provide in a Request: The pre-filing meeting request should identify the appropriate USACE permit (if available) and contain a narrative description of the project activities, project design plans and any available water quality information, including Waters of the U.S. delineations. Based on the information provided, the department will determine if a meeting is required. 
   • Topics to Discuss: If a determination is made that a pre-filing meeting is necessary, the project proponent and the department will discuss the nature of the proposed project and potential water quality effects; information needed to sufficiently ensure compliance with the Missouri Clean Water Law; potential National Pollutant Discharge Elimination System (NPDES) permitting; receiving stream conditions; compensatory wetland and/ or stream mitigation information; the anticipated timeline for construction and operation; and timing of the 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 satisfied the pre-filing meeting requirements, the WQC may be requested. WQC requests should be sent to the department’s WQC general email account at wpsc401cert@dnr.mo.gov. Per the federal 2023 Certification Rule and state regulations (10 CSR 20-6.060), the following requirements must be met in order to have a complete request for 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)(2)]: 
     • Identify which Nationwide Permit(s) and/ or General Permit(s) the USACE is using for project authorization
     • Provide any readily available water quality-related materials
   • 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) 
       • Missouri Stream Mitigation Method Adverse Impact Worksheets
       • Name of Mitigation Bank or In-Lieu Fee Provider
       • Location of Mitigation Site 
       • Permittee-Responsible: Permittee-Responsible mitigation plans should be reviewed and approved by the department before 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 feet of stream, acres of wetland, etc.) 
     • Equipment or measures planned to treat, control or manage discharge
   • Request Review: The department will review the WQC request and determine if requirements for a complete request were met and sufficient information was provided to certify the project will comply with Missouri water quality requirements [40 CFR § 121.1(j)]. 
     • If the request is determined to be incomplete: The reasonable period of time does not start. The department will request further information necessary to satisfy complete request requirements in order to begin. Failure or refusal to provide additional information to fulfill a complete request prevents the process from starting.  
     • If the request is determined to be complete: The department will provide a notification to the project proponent and the appropriate USACE district that a complete request was received. The reasonable period of time begins the date the complete request was made. The department may request additional information to ensure compliance with water quality requirements. Failure or refusal to provide additional information upon request may result in the denial of WQC or a request for extension of the reasonable period of time if the state cannot certify that the discharge will comply with water quality requirements.
3. Reasonable Period of Time: The WQC clock starts once a complete request for WQC is received by the department [40 CFR §121.6(a)]. The federal agency and the certifying authority may jointly agree, in writing, to a reasonable period of time to act on the complete request for certification [40 CFR §121.6(b)]. The default reasonable period of time is 60 days from the date of the complete request, unless an alternative date is identified by the department. It shall not exceed one year [33 U.S.C. §1341(a)(1)]. If the federal agency and the department do not agree in writing on the identified alternative reasonable period of time, the reasonable period of time shall be six months [40 CFR §121.6(c)].
   • If circumstances require a longer period of time than originally agreed upon, the federal agency and the department may agree, in writing, to extend the reasonable period for any reason [40 CFR §121.6(e)]. This might occur if the department requests additional information, if project plans change during the review or other unforeseen circumstances occur.
   • The reasonable period of time is extended automatically to accommodate the department’s public notice procedures or force majeure events (including, but not limited to, government closure or natural disasters), upon written notification by the department to the federal agency [40 CFR §121.6(d)]. 
4. Draft WQC: Once the department receives a complete request with sufficient information about the proposed project and its discharge, the WQC will be drafted, reviewed and, if appropriate, approved by the Water Protection Program. 
5. MoDNR Public Notice: The draft WQC will then be placed on public notice, typically for 21 days. If substantive comments are received, they will receive a response and the WQC will be updated if necessary. Substantive changes to the draft WQC may require another public notice and an extension of the reasonable period of time. 
6. Issue WQC: After the department’s 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 project proponent and the federal agency. WQC conditions become part of the federal permit [33 U.S.C. §1341(d)]. 
7. 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 did not require an Environmental Impact Statement or an Environmental Impact Statement resulted in a Finding of No Significant Impact. 
   • Fee: $1,500 - Projects did require an Environmental Impact Statement that did not result in a Finding of No Significant Impact. 
8. Modifications: WQCs are for plans as submitted, reviewed and certified in compliance with the procedures defined in the 2023 Certification Rule. Any project plans omitted from the request for WQC or any future project expansions or modifications may require a new WQC or a modification of the existing WQC. 
   • Project Modifications: Contact the appropriate USACE district to determine if a modification of project plans requires a permit modification. Contact the department to determine if a modification of project plans requires a WQC modification. Contacting both agencies concurrently is preferred.  
   • Undisclosed Information Discovered: Where the project proponent becomes aware that it failed to submit any relevant facts in a WQC request, or submitted incorrect information in a WQC request or in any report to the department, it shall promptly submit such facts for information. The department will determine whether the WQC covers the undisclosed activity, if it needs to be modified or if a new WQC is required. 
   • The federal agency and the department must agree, in writing, in order to modify a WQC. Only agreed upon portions of the WQC may be modified. The department cannot modify a WQC to revoke a grant of WQC or change a grant of WQC into a denial or waiver of WQC. [40 CFR §121.10].
9. 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].