How to Obtain an Individual Water Quality Certification for Individual Permits - PUB3029

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) Individual Permits.

Individual WQC for Individual Permits:

1. Start Process: Applicant submits an application to the USACE, and an individual permit is being utilized. 
2. USACE and Department Joint Public Notice: The USACE will publish a joint public notice for the project on behalf of the department. This satisfies the department’s public notice requirements [10 CSR 20-6.060(3) and 33 U.S.C. §1341(a)(1)]. This public notice provides the public an opportunity to provide their written comments regarding the proposed project. 
3. Pre-filing Meeting Request: Per the federal 2023 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]. 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 [Chapter 644, RSMo], potential 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.
4. MoDNR Comments: The department will review information in the Joint Public Notice and provide comments. This is generally the department’s first opportunity to review the project. The department provides two types of comments on USACE Public Notices. 
   • Comments that Do Not Require a Response: These are a preview of the conditions the department may place in the WQC when drafted and relevant information about the receiving stream. This is an opportunity for the project proponent and/or the USACE to review and determine if they have any concerns with potential WQC conditions. 
   • Comments that Require a Response: These are statements of additional information that will be required prior to WQC request or at the time of WQC request (e.g., antidegradation, compensatory mitigation, etc.); any concerns the department might have; and other applicable permitting that may be required (such as CWA Section 402 permits). The response to these comments provides sufficient information and clarifications for a request for WQC. This helps the department and the project proponent ensure all regulatory requirements will be met and sufficient information to draft the WQC is provided. 
5. Response to Comments: The USACE provides the comments to the applicant and the applicant must respond to comments. The response from either the applicant or the federal agency should be sent directly to the department’s general WQC email account at wpsc401cert@dnr.mo.gov.  
6. Alternatives Analysis: The USACE will perform the 404(b)(1) review for the project. This review must: 1) Make a determination that the proposed discharges are unavoidable (i.e., necessary); 2) Examine alternatives to the proposed activity and authorize only the least environmentally damaging practicable alternative; and 3) Require compensatory wetland and /or stream mitigation for all impacts associated with the activity. 
   • To limit duplication, documents produced as part of the USACE’s 404(b)(1) process will satisfy this component; the department will rely upon information contained in these documents to draft a WQC. The department will review any applicable alternatives analysis for compliance with the Missouri antidegradation requirement that waters of the state shall be maintained and protected. 
   • At a minimum, the alternatives analysis for the project should include: 1) At least one alternative to the proposed design or location of the project; 2) A no-action alternative to establish purpose and need for the project, and 3) An explanation why the proposed action is the most feasible. The department may request additional information. 
   • Contact the appropriate USACE district for information over the 404(b)(1) alternatives analysis requirements.
7. Complete WQC Request: Once the applicant has finalized project plans, knows what permit the USACE will utilize 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)(1)]: 
     • A copy of the federal permit application submitted to the federal agency.  
     • Provide any readily available water quality-related materials that informed the development of the application. 
   • 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) 
       1. Missouri Stream Mitigation Method Adverse Impact Worksheets
       2. Name of Mitigation Bank or In-Lieu Fee Provider
       3. Location of Mitigation Site 
       4. Permittee-Responsible: Permittee-Responsible mitigation plans should be reviewed and approved by the department prior to 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 ft of stream, acres of wetland, etc.)
     • Equipment or measures planned to treat, control, or manage discharge
   • Complete Request - Antidegradation Review (Alternatives Analysis) [10 CSR 20-7.031(3)]: The decision-making process for section 404 Individual Permits is contained in the 404(b)(1) guidelines [40 CFR Part 230] and contains all of the required elements department review. Because the 404(b)(1) guidelines meet these requirements, the department will not conduct a separate review for the proposed activity. The review requirement will be met through section 401 certification of individual section 404 permits and will rely upon the information contained in the 404(b)(1) findings document [10 CSR 20-7.031(3)(D)]
   • 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.
8. 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)].
9. Draft and Approval of 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 approved by the Water Protection Program. 
10. Issue WQC: Once 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)].
11. 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. 
12. 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 and contact the department to determine if a modification of project plans requires a WQC modification. Contacting both agencies concurrently is preferable.  
    • 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 or 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].
13. 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].