Section 401 Water Quality Certification for Pond Projects

Key points

• AgencyUnder Clean Water Act section 401(a)(1), anyone applying for a Federal license or permit for an activity (including construction or operation of facilities) that may result in any discharge into the navigable waters must give the permitting agency a certification from the State where the discharge originates or will originate (or, if appropriate, from the interstate water pollution control agency with jurisdiction at the discharge point) that the discharge will comply with the listed Clean Water Act sections. The State or interstate agency must establish public-notice procedures for all certification applications. Where a State or interstate agency has no authority to certify, the certification comes from the EPA Administrator.

  Applies when: Any Federal license or permit for an activity that may result in a discharge into navigable waters (for example, a Corps Section 404 permit for a discharge of dredged or fill material, such as fill for a pond dam, in a regulated water) 33 U.S.C. 1341(a)(1) (CWA section 401(a)(1)) [1]
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  Any applicant for a Federal license or permit to conduct any activity including, but not limited to, the construction or operation of facilities, which may result in any discharge into the navigable waters, shall provide the licensing or permitting agency a certification from the State in which the discharge originates or will originate...shall establish procedures for public notice in the case of all applications for certification...In any case where a State or interstate agency has no authority to give such a certification, such certification shall be from the Administrator.

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• RequirementCurrent 40 CFR part 121 (eCFR source note: 88 FR 66661, Sept. 27, 2023, i.e., the 2023 Rule) requires certification or waiver for any Federal license or permit that authorizes any activity which may result in any discharge from a point source into waters of the United States. The certifying authority's review is limited to the water quality-related impacts from the activity subject to the Federal license or permit, including the activity's construction and operation. EPA (the Administrator) certifies or waives where no state, Tribe, or interstate agency has authority to certify.

  Applies when: Any Federal license or permit (e.g., Corps Section 404 individual permit or NWP) for an activity that may discharge from a point source into waters of the United States 40 CFR 121.2; 40 CFR 121.3(a); 40 CFR 121.16(a) [2]
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  Source: 88 FR 66661, Sept. 27, 2023, unless otherwise noted...Certification or waiver is required for any Federal license or permit that authorizes any activity which may result in any discharge from a point source into waters of the United States...The certifying authority's evaluation is limited to the water quality-related impacts from the activity subject to the Federal license or permit, including the activity's construction and operation...Certification or waiver by the Administrator is required where no state, Tribe, or interstate agency has authority to give such a certification.

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• StatusPROPOSED ONLY (not in effect): EPA's Section 401 web page (last updated July 29, 2026) says EPA announced proposed revisions to the existing section 401 water quality certification regulations on January 13, 2026, and that the public comment period closed February 17, 2026. The page also states that the Clean Water Act gives states and authorized Tribes authority to grant, deny, or waive certification of proposed federal licenses or permits that may discharge into waters of the United States.

  EPA, Section 401 of the Clean Water Act (web page) [4]
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  The Clean Water Act gives states and authorized Tribes the authority to grant, deny, or waive certification of proposed federal licenses or permits that may discharge into waters of the United States...On January 13, 2026, the EPA announced proposed revisions to the existing Section 401 water quality certification regulations. The public comment period closed on February 17, 2026...Last updated on July 29, 2026

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• TimelineIf the State, interstate agency, or EPA fails or refuses to act on a certification request within a 'reasonable period of time (which shall not exceed one year)' after receiving it, the certification requirement is waived for that Federal application. No Federal license or permit may be granted until certification has been obtained or waived, and none may be granted if certification has been denied. Under section 401(d), a certification must set forth the effluent limitations, other limitations, and monitoring requirements necessary to assure that the applicant will comply with the applicable limitations and standards, and the certification becomes a condition on the Federal license or permit.

  Applies when: Any Federal license or permit subject to CWA section 401 33 U.S.C. 1341(a)(1); 33 U.S.C. 1341(d) [1]
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  fails or refuses to act on a request for certification, within a reasonable period of time (which shall not exceed one year) after receipt of such request, the certification requirements of this subsection shall be waived with respect to such Federal application. No license or permit shall be granted until the certification required by this section has been obtained or has been waived as provided in the preceding sentence. No license or permit shall be granted if certification has been denied...Any certification provided under this section shall set forth any effluent limitations and other limitations, and monitoring requirements necessary to assure that any applicant for a Federal license or permit will comply...and shall become a condition on any Federal license or permit subject to the provisions of this section.

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• StatusFINAL / IN FORCE: EPA's 'Clean Water Act Section 401 Water Quality Certification Improvement Rule' (the 2023 Rule, 88 FR 66558, published September 27, 2023) revised and replaced the 2020 section 401 regulations and took effect November 27, 2023. (fed-401-006 shows the current eCFR text of 40 CFR part 121 is sourced to this rule; fed-401-004 and fed-401-005 cover the pending 2026 proposal.)

  Applies when: All section 401 certification requests nationwide 88 FR 66558 (Sept. 27, 2023), FR Doc. 2023-20219, DATES and SUMMARY [6]
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  the Agency is finalizing a rule revising and replacing the 2020 regulatory requirements for water quality certification under Clean Water Act (CWA) section 401...DATES: This action is effective on November 27, 2023.

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• StatusPROPOSED ONLY: EPA's January 15, 2026 proposed rule 'Updating the Water Quality Certification Regulations' (91 FR 2008, RIN 2040-AG47; comments were due February 17, 2026) would revise several procedural and substantive parts of the 2023 Rule. Among other changes, proposed 40 CFR 121.3 would limit the scope of a section 401 certification to assuring that a discharge from the federally licensed or permitted activity complies with applicable and appropriate water quality requirements (the current 2023 text evaluates the 'activity'; see fed-401-006). The preamble notes the 2023 Rule has been subject to litigation for most of the time it has been in effect: Louisiana, et al. v. EPA, No. 2:23-cv-01714 (W.D. La.).

  Applies when: Would apply only if and when EPA finalizes it 91 FR 2008 (Jan. 15, 2026), FR Doc. 2026-00754, DATES, sec. I.A, n.26, and proposed 40 CFR 121.3 [7]
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  Comments must be received on or before February 17, 2026...would revise several procedural and substantive aspects of the Clean Water Act Section 401 Water Quality Certification Improvement Rule...the 2023 Rule has been in effect for less than two years and subject to litigation for most of that time. Louisiana, et al., v. EPA, No. 2:23-cv-01714 (W.D. La.)...The scope of a Clean Water Act section 401 certification is limited to assuring that a discharge from a federally licensed or permitted activity will comply with applicable and appropriate water quality requirements.

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Requesting certification and the decision deadline

EPA's rule requires the project proponent to request a pre-filing meeting with the certifying authority at least 30 days before submitting a certification request, unless the certifying authority waives or shortens that requirement. [2]

For an individual federal license or permit, the request must be in writing, signed, and dated. It must include a copy of the permit application submitted to the federal agency (for example, the Corps) and any readily available water quality-related materials that informed the application. [2]

Under EPA's rule, the reasonable period of time starts on the date the certifying authority receives the request. The federal agency and the certifying authority may jointly agree in writing on its length, but it cannot exceed one year from receipt; if they do not agree in writing, it is six months. The period is extended by the time needed for the certifying authority's public-notice procedures or a force majeure event (on written notice before the period ends), but never beyond one year from receipt. [2]

EPA's rule says a certifying authority may act on a request in one of four ways: grant certification, grant certification with conditions, deny certification, or expressly waive certification. If it determines that no water quality requirements apply to the activity, it must grant certification. Other than by the certifying authority's express waiver, the certification requirement is waived only if the certifying authority fails or refuses to act on the request within the reasonable period of time. [2]

For Corps permits, the Corps' own regulation says a waiver may be explicit, or is deemed to occur if the certifying agency fails or refuses to act within sixty days after receiving a request, unless the district engineer determines a shorter or longer period is reasonable (a longer period may not exceed one year). That sixty-day default differs from EPA's six-month default when no period is agreed in writing (see the conflict noted in this section). The Department of the Army permit form (33 CFR part 325, Appendix A) says that if a conditioned water quality certification has been issued for the project, the permittee must comply with its conditions as special conditions of the Corps permit. [2][8]

• ProcessBefore asking for certification, the project proponent must request a pre-filing meeting with the certifying authority at least 30 days before submitting the certification request, unless the certifying authority waives or shortens that requirement. For an individual Federal license or permit, the certification request must be in writing, signed, and dated, and must include a copy of the Federal permit application submitted to the Federal agency (e.g., the Corps) and any readily available water quality-related materials that informed the application.

  Applies when: Project-specific (individual) certification requests, including a Corps individual permit or a project-specific certification needed to use a Nationwide Permit 40 CFR 121.4; 40 CFR 121.5(a)(1) [2]
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  The project proponent shall request a pre-filing meeting with the certifying authority at least 30 days prior to submitting a request for certification...unless the certifying authority waives or shortens the requirement...If the request for certification is for an individual Federal license or permit, it shall be in writing, signed, and dated and shall include the following: (i) A copy of the Federal license or permit application submitted to the Federal agency; and (ii) Any readily available water quality-related materials that informed the development of the application.

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• TimelineThe 'reasonable period of time' for the certifying authority to act starts on the date it receives the certification request. The Federal agency (e.g., the Corps) and the certifying authority may jointly agree in writing on the period, but it cannot exceed one year from receipt. If they do not agree in writing, the default is six months. The period is extended by the time needed for the certifying authority's public-notice procedures or a force majeure event (on written notice before the period ends), but never beyond one year from receipt.

  Applies when: All section 401 certification requests under the 2023 Rule 40 CFR 121.6(a)-(d) [2]
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  The reasonable period of time begins on the date that the certifying authority receives a request for certification...The Federal agency and the certifying authority may jointly agree in writing to the reasonable period of time...provided the reasonable period of time does not exceed one year...do not agree in writing on the length of the reasonable period of time, the reasonable period of time shall be six months...the reasonable period of time shall be extended by the period of time necessitated by public notice procedures or the force majeure event.

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• ProcessA certifying authority may act on a request in one of four ways: grant certification, grant certification with conditions, deny certification, or expressly waive certification. If it determines no water quality requirements apply to the activity, it must grant certification. The certification requirement is waived only if the certifying authority fails or refuses to act within the reasonable period of time.

  40 CFR 121.7(a), 121.7(g); 40 CFR 121.9(a) [2]
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  A certifying authority may act on a request for certification in one of four ways: grant certification, grant certification with conditions, deny certification, or expressly waive certification...If the certifying authority determines that no water quality requirements are applicable to the activity, the certifying authority shall grant certification...The certification requirement shall be waived only if a certifying authority fails or refuses to act on a request for certification within the reasonable period of time.

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• TimelineFor Corps permits, the Corps' own regulation says a waiver may be explicit, or is deemed to occur if the certifying agency fails or refuses to act within sixty days after receiving a request, unless the district engineer determines a shorter or longer period is reasonable; any longer period may not exceed one year. The DA permit form in Appendix A to 33 CFR part 325 states that if a conditioned water quality certification has been issued for the project, the permittee must comply with its conditions as special conditions of the Corps permit.

  Applies when: Corps Section 404 (and Section 10) permits, including individual permits for pond dams or fill in regulated waters 33 CFR 325.2(b)(1)(ii); 33 CFR part 325, Appendix A (permit form), General Condition 5 [8]
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  A waiver may be explicit, or will be deemed to occur if the certifying agency fails or refuses to act on a request for certification within sixty days after receipt of such a request unless the district engineer determines a shorter or longer period is reasonable for the state to act...will determine a longer reasonable period of time, not to exceed one year...If a conditioned water quality certification has been issued for your project, you must comply with the conditions specified in the certification as special conditions to this permit.

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Nationwide Permits, including NWP 40 farm ponds

In the 2026 Nationwide Permits final rule (published January 8, 2026; the NWPs took effect March 15, 2026 and expire March 15, 2031), the Corps states that NWPs 15, 16, 17, 18, 21, 25, 29, 30, 34, 39, 40, 41, 42, 43, 46, 49, 50, and 59 authorize activities that may result in discharges, so section 401 certification or waiver is required for them. [3]

NWP 40 (Agricultural Activities) is on that list. Among other things, it authorizes construction of farm ponds in non-tidal waters of the United States, excluding perennial streams, provided the pond is used solely for agricultural purposes; it does not authorize construction of aquaculture ponds. [3]

If a state, authorized Tribe, or EPA denied certification for the issuance of an NWP, discharges are not authorized by that NWP unless and until the project proponent obtains certification for the specific discharge from the certifying authority or a waiver occurs. Under NWP General Condition 25(b), if the NWP activity requires pre-construction notification and the certifying authority has not previously certified the NWP under section 401, the activity that may result in a discharge is not authorized by the NWP until certification is obtained or waived. [3]

The Corps' NWP regulations say that if a state denies a required 401 certification for an activity that otherwise meets the terms and conditions of an NWP, that NWP's authorization for all such activities in the state is denied without prejudice until the state issues an individual 401 certification or waives. For those NWPs, after receiving an activity-specific certification request the district engineer sets a reasonable period (generally 60 days), after which the district engineer presumes the state has waived; the period may never exceed one year. [9]

NWP General Condition 27 requires every NWP activity to comply with any case-specific conditions added by the state, Tribe, or EPA in its section 401 water quality certification, as well as any regional conditions added by the Corps division engineer. [3]

• ProcessIn the 2026 Nationwide Permits final rule (published January 8, 2026), the Corps states that NWPs 15, 16, 17, 18, 21, 25, 29, 30, 34, 39, 40, 41, 42, 43, 46, 49, 50, and 59 authorize activities that may result in discharges, so section 401 certification or waiver is required for them. NWP 40 (Agricultural Activities) is on that list; it also authorizes construction of farm ponds in non-tidal waters of the United States, excluding perennial streams, provided the farm pond is used solely for agricultural purposes, and it does not authorize the construction of aquaculture ponds.

  Applies when: Farm ponds built under NWP 40 (non-tidal waters, not perennial streams, used solely for agricultural purposes; not aquaculture ponds); other pond work under NWPs on the list Reissuance and Modification of Nationwide Permits, 91 FR 768 (Jan. 8, 2026), FR Doc. 2026-00121: preamble sec. F (Section 401 of the CWA), 91 FR 850; NWP 40, 91 FR 868 [3]
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  Nationwide permits 15, 16, 17, 18, 21, 25, 29, 30, 34, 39, 40, 41, 42, 43, 46, 49, 50, and 59 authorize activities that may result in discharges and therefore 401 WQC or waiver is required for those NWPs...40. Agricultural Activities. Discharges of dredged or fill material into non-tidal waters of the United States for agricultural activities...This NWP also authorizes the construction of farm ponds in non-tidal waters of the United States, excluding perennial streams, provided the farm pond is used solely for agricultural purposes. This NWP does not authorize the construction of aquaculture ponds.

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• ProcessIf a state, authorized Tribe, or EPA denied water quality certification for the issuance of an NWP, discharges are not authorized by that NWP unless and until the project proponent obtains certification for the specific discharge from the certifying authority or a waiver occurs. Under NWP General Condition 25(b), if the NWP activity requires pre-construction notification and the certifying authority has not previously certified the NWP under section 401, the activity that may result in a discharge is not authorized by the NWP until certification is obtained or waived.

  Applies when: Using a 2026 Nationwide Permit where certification for that NWP was denied or not previously granted FR Doc. 2026-00121, 91 FR 768 (Jan. 8, 2026): preamble sec. F, 91 FR 851; NWP General Condition 25(b), 91 FR 880 [3]
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  If a certifying agency denied WQC for the issuance of an NWP, then the proposed discharges are not authorized by that NWP unless and until a project proponent obtains WQC for the specific discharge from the certifying authority, or a waiver of WQC occurs...If the NWP activity requires pre-construction notification and the certifying authority has not previously certified compliance of an NWP with CWA section 401...is not authorized by an NWP until water quality certification is obtained or waived.

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• ProcessCorps NWP regulations: if a state denies a required 401 certification for an activity that otherwise meets an NWP, that NWP's authorization for all such activities in the state is denied without prejudice until the state issues an individual 401 certification or waives. For NWPs where the state denied certification, the district engineer sets a reasonable period after receiving the activity-specific certification request (generally 60 days), after which the district engineer presumes state waiver; the period may never exceed one year.

  Applies when: Nationwide Permit activities in a state that denied 401 certification for that NWP 33 CFR 330.4(c)(3); 33 CFR 330.4(c)(6) [9]
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  If a state denies a required 401 water quality certification for an activity otherwise meeting the terms and conditions of a particular NWP, that NWP's authorization for all such activities within that state is denied without prejudice until the state issues an individual 401 water quality certification or waives its right to do so...reasonable period of time after receipt of the request for an activity-specific 401 water quality certification (generally 60 days), upon the expiration of which the DE will presume state waiver...but in no event shall the period exceed one (1) year

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