In October 2021, a federal district court issued a decision vacating the 2020 Clean Water Act Section 401 Certification Rule (“2020 Rule”), a Clean Water Act (“CWA”) regulation adopted by the Trump Administration in July 2020. The purpose of the rule was to “increase the predictability and timeliness” of CWA permitting by clarifying the authority of states and tribes under section 401 of the CWA. Ultimately, the 2020 Rule was vacated after a court’s finding that EPA would not readopt the rule, and that it ran contrary to a decision from the United States Supreme Court.

Section 401 of the CWA

What is recognized today as the modern CWA was originally adopted in 1972 as a series of amendments to the Federal Water Pollution Control Act of 1948. The 1972 amendments were adopted in response to a growing concern over the state of the nation’s waterways following a large oil spill off the coast of California, and a fire on the surface of the Cuyahoga River in northeast Ohio. The objective of the CWA of 1972 is to “restore and maintain the chemical, physical, and biological integrity of that Nation’s waters.” 33 U.S.C. § 1251(a). To achieve that goal, the CWA employs a variety of permitting systems that regulate pollution, including the National Pollutant Discharge Elimination System which requires permits for discharges of pollutants into waters protected by the CWA, and permits for the discharge of dredged and fill material into wetlands and other protected waterbodies.

Prior to receiving a permit to discharge into a water protected under the CWA, the permit applicant must obtain a water quality certification from the state or authorized tribe with jurisdiction over where the discharge would occur. This requirement comes from section 401 of the CWA and is aimed at ensuring that the proposed discharge would not violate state and tribal water quality requirements, or other CWA requirements. Under the CWA, water quality standards are set at the state level. Section 401 recognizes this, and provides a process for federal agencies to check in with states and allow them to certify that any proposed project will not violate water quality standards.

States and tribes may choose to grant, grant with conditions, or deny certification requests. When determining whether to grant certification, states and tribes will consider whether the proposed activity satisfies a variety of requirements, including effluent limitations standards, water quality standards, and “any other appropriate requirement of state [or tribal] law.” 33 U.S.C. § 1341(d). If a certification request is denied, then the accompanying permit will not be issued. 33 U.S.C. § 1341(a)(1). If the state grants a certification request with conditions, those conditions should be “necessary to insure compliance with applicable water quality requirements.” 33 U.S.C. § 1341(a)(2). Once a certification request has been submitted to the appropriate state or tribe, it has a “reasonable period of time” to issue a response, otherwise the certification requirements will be waived. 33 U.S.C. § 1341(a)(1). According to the statute, this period of time shall not exceed one year. 33 U.S.C. § 1341(a)(1).

Although not as well-known as other provisions of the CWA, section 401 plays an important role in the granting of CWA permits. Without state or tribal approval, a permit to discharge into a protected waterbody may not be issued.

2020 Certification Rule

In April 2019, the Trump Administration issued the Executive Order on Promoting Energy Infrastructure and Economic Growth (“EO 13868”). The Order stated that “[o]utdated Federal guidance and regulations regarding section 401 […] are causing confusion and uncertainty and are hindering the development of energy infrastructure.” It directed the Environmental Protection Agency (“EPA”) to revise the regulations implementing section 401 within 120 days. The regulations in place at the time had been originally adopted in 1971, a year before the 1972 amendments that made the CWA what it is today.

In response to EO 13868, EPA adopted a final rule in July 2020 that modified how section 401 was carried out. The new regulation made several key changes. First, the 2020 Rule formally established what is considered a “reasonable period of time.” Certifying authorities must determine the reasonable period of time to act on a certification request based on the complexity of the proposed project, the nature of the proposed discharge, and the potential need for additional study of water quality effects from the discharge. 40 C.F.R. § 121.16(c). While a reasonable period of time will be determined on a case-by-case basis, the amount of time will not exceed one year. 40 C.F.R. § 121.16(a).

The 2020 Rule also limits the scope of a certification decision to specific discharges from a proposed activity. Previously, certifying states and tribes could consider the water quality effects of the proposed activity as a whole. In PUD No. 1 of Jefferson Cty. v. Washington Dept. of Ecology, 511 U.S. 700 (1994), the Supreme Court concluded that a state had acted appropriately under section 401 when it granted a certification request with a condition that the project would maintain specific minimum stream flows in order to protect salmon and steelhead runs. The plaintiffs filed suit, arguing that the condition to maintain minimum stream flows was directed at the project itself, not the specific discharges associated with the project, and was therefore beyond the scope of what the state could require under section 401. The Supreme Court disagreed, citing the regulations for section 401 that were in place at the time which required certifying states and tribes to find that “there is a reasonable assurance that the activity will be conducted in a manner which will not violate applicable water quality standards.” Therefore, under section 401 states and tribes had the authority to grant certification with conditions that applied to the whole project instead of just the discharges that would occur as a result of the project. The 2020 Rule reversed this, limiting conditions to just specific discharges.

Finally, the 2020 Rule restricts the conditions that states and tribes may impose by limiting them to point source discharges into waters protected by the CWA, and no longer allowing conditions for nonpoint source discharges. Under the CWA, discharges of pollutants into protected waters are divided into two categories, point source and nonpoint source. A point source is defined as “any discernible, confined and discrete conveyance,” such as a pipe, ditch, or tunnel. 33 U.S.C. § 1362(14). A nonpoint source is any discharge that does not come from a point source, such as agricultural runoff or sediment from eroding streambanks. By limiting the conditions that certifying states and tribes can impose only to point source discharges into federally protected waters, the 2020 Rule restricted the ability of states and tribes to consider issues related to water protected under non-federal law.

The Court’s Decision

After the 2020 Rule went into effect, various states, tribes, and environmental groups filed suit against EPA to set aside the regulation. Among the lawsuits was In re: Clean Water Act Rulemaking, No. C 20-04636 WHA (N.D. Cal. 2021), a challenge filed by several environmental groups in a federal district court in Northern California.

After the Biden Administration took office in January 2021, the 2020 Rule was among several environmental regulations highlighted for review. Many of those regulations had been challenged by lawsuits. The Biden Administration asked courts across the country to end those lawsuits by sending the rules back to EPA for review, while allowing them to remain legally effective during the agency’s review process. The court in In re: Clean Water Act Rulemaking agreed to send the 2020 Rule back to EPA, but refused to let it remain in legal effect, agreeing with plaintiffs that vacatur was more appropriate.

In considering EPA’s request for voluntary remand of the 2020 Rule, the court noted that in the Ninth Circuit remand of an agency regulation without vacatur is appropriate only in limited circumstances. The decision on whether to vacate depends on (1) whether the regulation is so flawed that the agency would not readopt it after remand; and (2) the disruptive consequences of vacatur. The court applied this two-part test to the 2020 Rule. First, the court concluded that the 2020 Rule was so flawed that EPA would not adopt it again after remand and review. The court based that decision both on the rule being contradictory to the Supreme Court’s ruling in PUD No. 1 of Jefferson Cty. v. Washington Dept. of Ecology, and EPA’s acknowledgement that it does not intend to reinstate the 2020 Rule. Next, the court concluded that vacating the 2020 Rule would not have any significant disruptive consequences. The court reached this conclusion after noting that the 2020 Rule had only been in place for 13 months while the previous rule had been in place since 1971. The court was also persuaded by the plaintiffs’ allegations that “significant environmental harms” were “likely to transpire” without vacatur. Therefore, the court vacated the rule and sent it back to EPA for further review.

Going Forward

Following the court’s vacatur of the 2020 Rule, section 401 of the CWA will be carried out according to the 1971 regulations. Prior to the court’s decision, EPA had been conducting its own review of the 2020 Rule, and had begun work on further regulatory action. In May 2021, EPA announced that it would begin taking steps to “reconsider and revise” the 2020 Rule. Following that announcement, EPA conducted various listening sessions with stakeholders to receive feedback on section 401 implementation. It is currently unclear whether EPA intends to continue with its plan to draft a new section 401 rule after the court’s decision.


To read the court’s decision in In re: Clean Water Act Rulemaking, click here.

To read the 2020 Rule, click here.

To read the 1971 section 401 regulations, click here.

To read the section 401 of the CWA, click here.

For more National Agricultural Law Center resources on the CWA, click here.