EPA Proposes Major Changes to 401 Water Quality Certification

The U.S. Environmental Protection Agency (EPA) recently published a proposed rule to update and clarify several substantive and procedural requirements for the 401 water quality certification requirements of the Clean Water Act (CWA). 91 Federal Register 2008 (January 15, 2026) (“Proposed Rule”). Section 401 of the CWA authorizes “States to review for compliance with appropriate Federal, State, and Tribal water quality requirements any discharge into waters of the United States that may result from a proposed activity that requires a Federal license or permit.” Id. The public comment period ended February 17, 2026. 

401 Water Quality Certification

Under CWA, Section 401, a Federal agency may not issue a license or permit to conduct any activity that may result in any discharge into waters of the United States (such as a 404 permit to fill or drain wetlands or dam a stream), unless the State or authorized Tribe where the discharge would originate either issues a section 401 water quality certification or certification is waived for failure to issue a decision within one year of the application. Under the statute “a certifying authority may grant, grant with conditions, deny, or waive certification in response to a request from an applicant. The certifying authority determines whether the potential discharge or discharges from the proposed activity will comply with the applicable provisions of sections 301, 302, 303, 306, and 307 of the CWA and any other appropriate requirement of State law.” 91 Federal Register 2008, 2013. Certifying authorities also may add to a certification “any effluent limitations and other limitations, and monitoring requirements” necessary to assure compliance. Id. at 1341(d). These limitations and requirements must become conditions of the Federal license or permit should it be issued. 

Proposed Rule Changes to 401 Water Quality Certification Process

The Proposed Rule would narrow the 401 water quality certification review process dramatically. The changes fall into four categories. 

1.    Certainty in the Request for Certification

The Proposed Rule first clarifies when the statutory timeline for certification review starts. “In order for a request for certification to start the statutory timeline for review, it must meet the requirements as defined in this [Proposed Rule], rather than as defined by the certifying authority.” Id. at 2017. The Proposed Rule includes an enumerated list of documents and information to include in a request for certification for all Federal licenses or permits, including the following: (1) the Federal license or permit application submitted to the Federal agency or a copy of the draft Federal license or permit; (2) readily available water quality-related materials on any potential discharges from a point source into waters of the United States from the Federally licensed or permitted activity that informed the development of the application or draft license or permit; and (3) any additional project information as proposed in 40 CFR 121.5(c) not already included in the request for certification.

Under this proposed rulemaking, a request for certification must include all applicable components to start the statutory clock. States are no longer able to “blur” the “bright-line rule regarding the beginning of [the certification] review” process, which states the timeline for a certifying authority's action regarding a request for certification “shall not exceed one year.” Id. The Agency is also proposing to remove provisions allowing State and Tribal certifying authorities to define additional content in a request for certification.         

2.    Restricting 401 Water Quality Certification to the Discharge    

If finalized, the proposed rulemaking “would narrow the current regulation's broad activity-based scope of certifying authority review to what Congress clearly intended: an assessment of whether a facility's point source discharges into waters of the United States will comply with specified water quality requirements.” Id. at 2023. 

According to the Preamble, this application is consistent with CWA. The first sentence in CWA section 401(a)(1) provides that “[a]ny 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 . . . that any such discharge will comply with the applicable provisions of sections 301, 302, 303, 306, and 307 of this Act” (emphasis added). “The use of the phrase “such discharge” in the very sentence that identifies what a State must certify is strong textual support for EPA's proposed interpretation.” Citing, Park 'N Fly, Inc. v. Dollar Park & Fly, Inc., 469 U.S. 189, 194 (1985) (“Statutory construction must begin with the language employed by Congress and the assumption that the ordinary meaning of that language accurately expresses the legislative purpose.”); PG&E v. FERC, 113 F.4th 943, 948 (D.C. Cir. 2024) (explaining that, “when ‘addressing a question of statutory interpretation, we begin with the text'”) (quoting City of Clarksville v. FERC, 888 F.3d 477, 482 (D.C. Cir. 2018)).

Conversely, EPA states 401(a)(1) of the CWA uses the term “activity” to describe the type of Federal license or permit that triggers CWA section 401 certification—namely, 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.” Id.  “[I]f a federal license or permit to conduct an activity may result in a discharge, then the certifying authority would certify that any such discharge will comply with the enumerated provisions of the CWA.” Id.

This approach is bolstered by other changes to the 401 regulations. The Proposed Rule would remove the requirement for “conditions” necessary to ensure compliance with the 401 programs. A certifying authority certifies compliance with “water quality requirements.” “Water quality requirements” would be defined as “applicable provisions of sections 301, 302, 303, 306, and 307 of the Clean Water Act, and applicable and appropriate state or tribal water quality-related regulatory requirements for discharges” to ensure activity-based requirements do not creep back into the regulations. And, under the Agency's proposal, “certifying authorities cannot consider water quality impacts to waters beyond waters of the United States, or impacts from outside the discharge itself.” 91 Federal Register at 2027.

3.    Contents of a Certification Decision

As if to ensure activity-based regulations do not return, the Proposed Rule would also require each certification decision include a statement indicating whether the discharge will comply with water quality requirements, and if not, supporting information. In circumstances where a certifying authority grants certification with conditions, EPA proposes each condition includes an explanation why the condition is necessary to assure the discharge(s) from the proposed project will comply with water quality requirements, and a citation to the applicable water quality requirement upon which the condition is based. In circumstances where certification is denied, written notification of denial must include “the specific water quality requirements with which the discharge(s) will not comply; a statement explaining why the discharge will not comply with the identified water quality requirements; or if the denial is due to insufficient information, a description of any missing water quality-related information.” Id. 

Next Steps: Application of the Statute

After public comments are reviewed, a final rule may be issued. Certifying authorities like States and Tribal lands may then revise applicable requirements to be no less stringent than the EPA requirements. In the meantime, applicants for 401 water quality certifications may wish to rely on EPA interpretation of the CWA to argue conditions in 401 water quality certifications going beyond the impacts to water quality by “discharges” may exceed the scope of the CWA and implementing regulations.