On January 15, 2026, the US Environmental Protection Agency proposed updates to the water quality certification process under Section 401 of the Clean Water Act. Section 401 authorizes States and Tribes to review projects involving a discharge into waters of the United States and certify their compliance with water quality requirements, before a federal permit is issued. The new rule comes in response to a 2023 rule issued by the Biden Administration, which broadened the scope of certification review, among other changes to the program.  

According to EPA, the new rule is designed to increase transparency, efficiency, and predictability for certifying authorities and the regulated community, and will better align with the text and legislative history of the Clean Water Act. The following proposals are among the most significant revisions to the current regulations:  

• Defining all documents and information that must be included in a request for certification to initiate 401 review. Whereas States and Tribes previously could require additional components in a request, the new rule provides a single standardized list of materials that, once submitted, will start the one-year statutory clock to act on a 401 certification.  

• Narrowing the scope of certification review from the “activity as a whole” to the “point source discharge” alone. In a departure from the 2023 rule, EPA is proposing to shift 401 review from the entire activity subject to the federal permit to the discharges of that activity. Relatedly, the new rule would allow certifying authorities to consider water quality impacts only to waters of the United States, not to any waters beyond federal regulation. 

• Requiring certifying authorities to explain in writing the basis of their certification decisions. Under the proposed rule, a State or Tribe must state whether it has chosen to grant, grant with conditions, deny, or expressly waive certification. In the case of certification with conditions, the decision document must explain each condition and cite the water quality requirement for which the condition is necessary to assure compliance. In the case of denial, the decision document must identify that water quality requirement that may be violated or, if denial is based on insufficient information, must describe any missing water quality-related information. 

• Requiring agreement by the federal agency, the certifying authority, and the applicant for any modification to a grant of certification. Whereas the 2023 rule allowed for modification by the certifying authority and the federal agency alone, the proposed rule includes a direct role for the applicant in the modification process, requiring the applicant’s consent to the fact and language of any modification.  

EPA is accepting public comments on its proposed rule until February 17, 2026. Meanwhile, the fate of 401 review is also being debated in Congress and in the courts. In December 2025, the US House approved permitting reform legislation that would similarly limit the scope of 401 review, although the Senate is unlikely to take up the measure. And a legal challenge to the Biden-era 401 rule remains pending in the Western District of Louisiana, with industry groups and GOP states claiming the rule exceeds EPA’s statutory authority under Section 401.