To go directly to our Defining Waters of the United States section click here.
To go directly to our Section 401 Water Quality Certification section click here.
Defining Waters of the United States
By Abby Husselbee and Anna Todd (JD 2023)
The Supreme Court’s decision in Sackett v. EPA has the potential to shape EPA’s authority to define what waters are protected under the Clean Water Act
The Clean Water Act (CWA) governs the discharge of pollutants into waters of the United States (WOTUS). Supreme Court decisions have, and will continue, to shape the breadth of agency authority under the act to define which waters are protected under the Act. Many of the ongoing disagreements over the scope of the agencies’ authority to define WOTUS relate to a 2006 case, Rapanos v. United States. In that case, there was no majority opinion. Instead, Justice Scalia wrote a 4-justice plurality opinion, and Justice Kennedy wrote a solo concurring opinion. The result has been confusion over which waters fall under the CWA since the circuit courts and administrations have interpreted Rapanos differently.
Justice Scalia’s opinion concluded that navigable waters, and thus WOTUS, cannot refer to channels that carry intermittent water, like ditches, because other sections of the CWA define such conduits as point sources. Justice Scalia also explained that including intermittent flows would impinge on powers that traditionally belong to the states and that “[w]e ordinarily expect a ‘clear and manifest’ statement from Congress to authorize an unprecedented intrusion into traditional state authority.” Thus, the plurality created a two-step test that would require wetlands to be adjacent to “relatively permanent” bodies, and would require the wetlands to have a “continuous surface connection” with these waters.” The Trump administration’s Navigable Waters Protection Rule relied on the plurality’s reasoning.
In contrast, Justice Kennedy’s concurrence established a relatively more flexible test. His test required “a significant nexus between the wetlands in question and navigable waters in the traditional sense” and that nexus should to be assessed with regard to CWA’s purpose and goals. The Obama administration’s Clean Water Rule adopted much of Justice Kennedy’s opinion.
On his first day in office, President Biden directed EPA and the Corps to review the Trump administration’s rule. Additionally, the US District of Arizona vacated the Navigable Waters Protection Rule, In response, the Biden administration began interpreting WOTUS “consistent with the pre-2015 regulatory regime.” However, EPA recognized that the status remained unsettled due to the 14 additional pending cases challenging the prior rules (the Obama administration rule, the rule repealing the Obama administration rule, and the Trump administration’s Navigable Waters Protection Rule). Therefore, EPA took the regulatory step in December 2021 to propose regulations that reflect the pre-2015 definition of WOTUS. EPA has also initiated a process to hear from stakeholders to support a second rulemaking step, which would refine the definition of WOTUS.
Most recently, however, the Supreme Court agreed to hear Sackett v. EPA (Sackett II), which will potentially shape EPA’s upcoming rulemaking by clarifying which of the Rapanos’ tests controls. The court heard the case on October 3, 2022, and will likely issue an opinion in 2023.
For more on this litigation and policy changes, see our Defining Waters of the United States/Clean Water Rule Regulatory Tracker page.
 The Supreme Court had considered this issue even before Rapanos. United States v. Riverside Bayview Homes Inc., 474 U.S. 121 (1985).
 In a plurality opinion, at least five justices agree on the result, but no legal reasoning is shared by enough justices to establish a majority.
 In the Rapanos case, the Court was split 4-1-4 with Chief Justice Roberts and Justices Thomas and Alito joining Justice Scalia’s opinion. Justice Kennedy wrote a solo concurrence, and Justice Stevens authored the dissent which Justices Souter, Ginsburg, and Breyer joined.
 Id. at 736.
 Id. at 738.
 Id. at 742.
 Id. at 779; 773.
 In EO 13990, President Biden also revoked an Executive Order by President Trump that had required EPA to review the 2015 rule. 86 Fed Reg. 7,037 (Jan. 20, 2021).
 Sackett v. Env’t Protection Agency, 8 F.4th 1075 (9th Cir. 2021), cert. granted Jan. 24, 2022.
Section 401 Water Quality Certification
By Abby Husselbee
EPA is working to finalize its updates to section 401 implementing regulations.
Section 401 of the Clean Water Act requires applicants seeking federal permits for activities that could result in a discharge to navigable waters to seek the approval of states, territories, or authorized tribes through a certification process. Under section 401, states, territories, and tribes can deny certification of projects that would violate the CWA, and the federal government cannot grant a permit if the state denies certification. States may also use section 401 to enforce their own water quality standards, which may be more stringent than federal standards.
EPA’s 1971 implementing regulations, which were effective until 2020, allowed the state or other certifying authority to review the environmental consequences of an “activity as a whole,” rather than only allowing states to review environmental impacts tied to each discharge. However, the Trump administration’s 2020 Clean Water Act Section 401 Certification Rule implemented a ”discharge-only” approach, which allowed states to consider only whether the discharge, rather than the water itself, meets water quality standards. The 2020 rule also forbade states from considering “…air quality or transportation concerns, public access to waters, energy policy, or other multi-media or non-water quality impacts….” and gave EPA the sole discretion to determine a reasonable timeline for state decisions, which the Trump EPA concluded was no more than one year. Several environmental groups, tribes, and states challenged the 2020 rule.
Upon entering office, President Biden directed EPA to review the 2020 rule, and in October 2021 the Northern District of California vacated the 2020 rule, remanding it to EPA, and reinstating the 1971 rule. Eight states intervened to appeal the decision to the Ninth Circuit, and on April 6, 2022, the Supreme Court stayed the lower court’s vacatur while the appeal is pending. As a result, it is expected that the 2020 rule remains effective until the Biden administration finalizes a replacement.
On June 2, 2022, EPA released proposed revisions to the section 401 implementing regulations that would adhere to the 1972 CWA. The proposal would allow states to consider the environmental impact of the activity as a whole (i.e., not only discharges). EPA justifies this wholistic review as consistent with a 1994 Supreme Court case, PUD No. 1 of Jefferson County, in which a seven-justice majority held that while a discharge is a predicate condition to trigger a section 401 review, section 401 allows states to consider the impact of the activity as a whole.
The proposal would allow EPA to work with states and tribes to determine what is a reasonable period of time to make a certifying decision. Additionally, EPA’s proposal makes clear that the agency “does not believe that the scope of a state’s or tribe’s certification review is limited only to water quality effects in bodies of water meeting the definition of ‘‘navigable waters’’ or waters of the United States, or to water quality effects caused by point sources.” Thus, EPA proposes that while the need for certification would be triggered by a potential discharge into federal waters (i.e., navigable waters), states would have the authority to consider whether the discharge will comply with various provisions of the CWA as well as “any other appropriate requirement of State or Tribal law.” However, similar to the 2020 rule, EPA also proposes to continue to prohibit states from making certification decisions based on air quality, traffic, noise, or other certification decisions not related to water quality. EPA also proposes to retain some the 2020 rule’s procedures and definitions.
Once EPA finalizes the rule, litigants opposing it are likely to focus on EPA’s authority to allow states to consider the “activity as a whole.” In their brief to the Supreme Court by the states seeking a stay of the Northern District of California vacatur of the 2020 rule, the states focused on meaning of the word “discharge” in the CWA. Although the Court did not reach this issue when it stayed the vacatur, it will be important for EPA’s final rule to ground its reasoning on “return[ing] to the scope of certification standard affirmed by the Supreme Court.”
Additionally, the role and authority of states, tribes, and EPA to review the potential water quality impacts from the project, including state and tribal requirements, will be a key issue in any litigation, especially depending on the decision in Sackett II discussed in our WOTUS section.
For more on this rule, see our Section 401 Water Quality Certification Regulatory Tracker page.
 33 USC § 1341(d); 1370.
 This approach was endorsed by seven justices of the Supreme Court in PUD No. 1 of Jefferson Cty. v. Washington Dept. of Ecology. 511 U.S. 700, 711–12 (1994) and affirmed by the Supreme Court in S.D. Warren Co. V. Maine Board of Envt. Protection. 574 U.S. 370 (2006).
 This approach had been endorsed by the two dissenting justices in PUD No. 1. 511 U.S. 700, 724 (Thomas, J., dissenting).
 The majority does not offer reasons for granting the application, but Justice Kagan authored a dissent in which Chief Justice Roberts and Justices Breyer and Sotomayor joined.
 EPA defines ”activity as a whole” as “any aspect of the project activity with the potential to affect water quality.” Clean Water Act Section 401 Water Quality Certification Improvement Rule, 87 Fed. Reg. 35,318, 35,435 (proposed June 9, 2022) (to be codified at 40 C.F.R. § 121, 122, 124).
 PUD No. 1, 511 U.S. 700, 711–12 (1994) (“EPA’s conclusion that activities-not merely discharges-must comply with state water quality standards is a reasonable interpretation of § 401, and is entitled to deference.”) Parties in recent cases have continued to disagree on whether discharge is a necessary condition or a limit to the scope of review. See Application for Stay, Louisiana v. American Rivers, No. 21A539 (2022).
 This decision would happen on a case-by-case basis. The CWA still sets outer bounds—a reasonable period of time cannot exceed one year. 33 U.S.C. § 1341(a)(1).
 87 Fed. Reg. at 35,348.
 87 Fed. Reg. at 35,324.