EPA Proposes Updates to Clean Water Act’s Water Quality Certification Requirements

By Sahana Rao and Private:

On August 8, 2019, the United States Environmental Protection Agency (“EPA”) published a set of proposed amendments (the “Proposed Rule”) to the regulations governing the issuance of Water Quality Certifications by states pursuant to Section 401 (“Section 401 Water Quality Certification”) of the Clean Water Act (“CWA”).

Under the Section 401 Water Quality Certification process, a state evaluates whether a proposed activity within its jurisdiction that a) requires a federal permit or license and b) may result in a discharge into navigable waters will comply with the CWA, as an element of cooperative federalism under the statute. The state reviews the project and either certifies, certifies with conditions, or declines to certify that the discharge for the certification will comply with applicable provisions of the CWA. The certification must also set forth any effluent limitations or monitoring requirements necessary to ensure that the applicant complies with the CWA, as well as “any other appropriate requirements of State law.”

The federal regulations governing Section 401 Water Quality Certifications have not been updated since before the last major overhaul of the CWA in 1972. In the decades since, states have broadly interpreted several aspects of these regulations. For instance, states must decide on certification “within a reasonable period of time (not to exceed one year) from receipt of a certification request” or certification is deemed waived. However, several states have taken the position in implementing the certification process that submission of any new information for a project restarts the one-year deadline. States have historically taken a wide-ranging approach to determining whether the certification requirement was triggered (that is, whether the project seeking a federal permit or license would potentially discharge to navigable waters) and what scope of review was required. Likewise, states have interpreted the term “discharge” to encompass not only point source discharges, like a particular pipe or outfall, but also non-point source discharges, like surface water runoff. The effluent limitations and monitoring requirements used to ensure compliance likewise stretched beyond restrictions based only on point-source discharges. Until now, this broad approach was supported by EPA guidance and relevant jurisprudence, including the U.S. Supreme Court’s 1994 decision in PUD No. 1 of Jefferson County v. Washington Department of Ecology, 511 U.S. 700 (1994).

Given the breadth of issues that could be considered to affect water quality under this approach, as well as the frequent resetting of deadlines, Section 401 review has been known to significantly slow or even sideline proposed projects—particularly energy-related projects, such as pipelines and hydropower projects. Earlier this year, the President issued Executive Order 13868, titled “Promoting Energy Infrastructure and Economic Growth,” which directed EPA to update the regulations governing Section 401 Water Quality Certification with an eye to clarifying the scope of review and facilitating expedient certification. In a sweeping reversal of past practice, EPA now proposes to considerably limit the scope of Section 401 Water Quality Certification, largely following the dissenting opinion of Justice Clarence Thomas in PUD No. 1. Some of the changes in the Proposed Rule were previewed in guidance that EPA issued on June 7, 2019 in response to the Executive Order.


First, EPA proposes that the state’s review under Section 401 “must be limited to considerations of water quality,” and to the specific point source discharge(s) that trigger the certification requirement and their potential impacts, rather than a broader evaluation of a project’s potential water quality impacts. The limited review would preclude considering indirect water quality concerns that states  previously included in their determinations, like air emissions impacts, and would prohibit conditions to certification that do not directly pertain to the water quality impacts from a potential point source discharge, such as public access for fishing, hiking or biking trails.

The Proposed Rule also allows for the federal agency in charge of the ultimate permit or license to weigh in on whether certification conditions fall within the scope of Section 401. If a federal agency communicates disagreement with a condition from the state and the issue is not timely resolved, that condition will not be included in the ultimate permit or license. The federal agencies would determine whether the state has provided information sufficient to support the conditions. EPA contemplates that the omission of “deficient” conditions would not invalidate the certification or other conditions therein.

EPA has also proposed measures to clarify the one-year deadline, which has been the subject of recent litigation.  The Proposed Rule sets forth specific factors establishing what constitutes a “certification request,” eliminating states’ ability to extend their deadline by assessing a request for certification as incomplete. The Proposed Rule would also deem the certification request waived by the state if a determination is not forthcoming by the one-year deadline.

These proposed limitations to Section 401 review significantly constrict the scope of issues that states or tribes can consider when assessing the potential water quality impacts of a project. However, the more streamlined scope of review and the increased clarity on deadlines allow for quicker evaluations by states and more certainty on timing for all parties involved. It remains to be seen whether the final rule will retain the characteristics described above and how it will bear out in practice.

EPA is currently seeking public comments on the Proposed Rule, which are due October 21, 2019. Stay tuned as SPR follows the development of these regulations.