Section 401 Water Quality Certification – Environmental and Energy Law Program

Current Status

EPA finalized a new rule to update Section 401 implementing regulations in September 2023. Louisiana and ten other states challenged the rule in federal court, and litigation is ongoing in the Western District of Louisiana.

Why It Matters

The Clean Water Act (CWA) is a bedrock environmental law intended to prevent discharges of pollutants into waters of the United States without a permit. States set water quality standards — designated uses for water bodies (e.g., water must be swimmable or fishable) with criteria to protect the designated uses. The CWA then provides mechanisms for states to enforce those standards.

CWA section 401 governs certification of water quality. Under section 401, any project seeking federal permits or licenses for activities that “may result in any discharge into the navigable waters” must also obtain a water quality certification from a state or interstate authority. Projects that trigger section 401 certification include projects requiring permits for disturbing wetlands, permits under the Rivers and Harbors Act, licenses for hydroelectric power plants, and licenses from the Nuclear Regulatory Commission. The certification process takes a holistic look at the water quality and the uses of the water where the discharge(s) may occur to ensure that water quality is maintained and that the water can support human, plant, and animal life.

Section 401 provides significant latitude to states to issue water quality certifications. States can approve projects without change, conditionally certify activities to reduce harm while allowing projects to move forward, deny certification, or waive the right to issue a certification (either affirmatively or by failing to promptly act). Crucially, if a state denies certification, federal agencies cannot permit such activity. In recent years, states have used their section 401 authority to deny permits to coal terminals, liquefied natural gas export facilities, and pipelines.

Key Resources

Timeline

Biden Administration

May 7, 2024 Parties submitted cross motions for summary judgment. Louisiana et al. v. EPA, Docket No. 2:23-cv-01714 (W.D. La). On the Feb. 11, 2025, the Court granted EPA a 90-day abeyance to allow the incoming administration to review the litigation.

Mar. 7, 2024 The Western District of Louisiana denied Louisiana’s Motion for Preliminary Injunction after hearing oral arguments on March 5. Louisiana et al. v. EPA, Docket No. 2:23-cv-01714 (W.D. La).

Jan. 24, 2024 The Western District of Louisiana sets the hearing on the Motion for Preliminary Injunction for March 5, 2024. Louisiana et al. v. EPA, Docket No. 2:23-cv-01714 (W.D. La).

Jan. 12, 2024 EPA filed a motion in opposition to the states’ motion preliminary injunction. Louisiana et al. v. EPA, Docket No. 2:23-cv-01714 (W.D. La).

Dec. 4, 2023 Eleven states sued EPA, asking the Western District of Louisiana to vacate and block enforcement of the new rule, arguing that EPA’s new rule exceeds the agency’s statutory authority. The states also filed a motion for preliminary injunction to block the rule. Louisiana et al. v. EPA, Docket No. 2:23-cv-01714 (W.D. La).

Sept. 27, 2023 EPA publishes the final rule, effective Nov. 27, 2023. The rule allows states to consider water quality impacts from the “activity subject to the Federal license or permit”. EPA removes the phrase “as a whole” in the final rule.

June 29, 2023 The District Court for the Northern District of California stays further proceedings until EPA publishes its final rule. In re Clean Water Act Rulemaking, Docket No. 3:20-cv-04636 (N.D. Cal.).

Feb. 21, 2023 The Ninth Circuit holds that the District Court lacked authority to vacate the 2020 401 Certification Rule without holding the rule unlawful. In re: American Rivers v. American Petroleum Institute (9th Cir.).

June 1, 2022 EPA proposes new regulations under Section 401. The proposed rule would restore the scope of state review, allowing states to consider water quality impacts from the “activity as a whole.” EPA receives nearly 300 comments on the proposal.

May 17-June 1, 2022 States, tribes, and environmental organizations file a Motion for Indicative Ruling in the Northern District of California. The parties ask the court to issue a ruling telling the Ninth Circuit that it will revisit its earlier vacatur order, a move that would allow the case to move forward on the merits. The court can grant the order if it finds extraordinary circumstances to justify the relief. EPA opposes the plaintiffs’ Motion for Indicative Ruling, urging the judge to allow the appeal to continue in the Ninth Circuit. In re Clean Water Act Rulemaking, No. 3:20-cv-04636 (N.D. Cal.).

Apr. 6, 2022 The Supreme Court grants the application of eight states and industry groups who asked the court to stay the N.D. Cal. ruling. This ruling reinstates the Trump administration’s 2020 revision to Section 401 of the Clean Water Act that limits the power of states and tribes to block permits for federal dams and energy projects. Specifically, the rule requires states to review projects within one year and to only consider water-quality when deciding to approve or reject projects. Louisiana, et. al., v. American Rivers, et. al., No. 21A539.

Feb. 25, 2022 The Ninth Circuit denies EPA’s motion to dismiss the appeal of the District Court’s In re Clean Water Act Rulemaking decision. The court also holds that the District Court’s ruling, which tossed the previous Trump-era rule, will remain in effect pending the appeal. In re Clean Water Act Rulemaking, Docket No. 21-16958 (9th Cir.).

Dec. 17, 2021 EPA publishes a document entitled “Clean Water Act Section 401 Water Quality Certification Questions and Answers on the 2020 Rule Vacatur.”

Dec. 7, 2021 The District Court in the Northern District of California denies the motion to stay the vacatur of the 2020 Certification Rule, so the 1971 rule remains in place. In re Clean Water Act Rulemaking, Docket No. 3:20-cv-04636 (N.D. Ca.).

Nov. 17-30 2021 Eight states and industry groups appeal the District Court’s vacatur of the 2020 Clean Water Act Section 401 Certification Rule and move to stay the ruling pending the appeal.EPA opposes the motion to stay the 2020 Certification Rule, announces that it is not appealing the court’s October decision, and confirms that it is still in the rulemaking process to update the 1971 rule. In re Clean Water Act Rulemaking, Docket No. 3:20-cv-04636 (N.D. Ca.).

Oct. 21, 2021 The District Court for the Northern District of California vacates and remands to the EPA the 2020 Clean Water Act Section 401 Certification Rule. The court’s ruling reinstates the previous 1971 Certification Rule. In re Clean Water Act Rulemaking, No. 20-cv-4636 (N.D. Ca.).

Aug. 6, 2021 The Eastern District Court of Pennsylvania remanding the 2020 rule to EPA without vacating the rule, instructing it to “expedite the resolution of this process so that any new rule will become effective as soon as possible.” Del. Riverkeeper Network v. EPA, No. 2:20-CV-3412 (E.D. Pa.).

Aug. 2-6 2021 The District of South Carolina granted EPA’s request to remand the 2020 rule to the agency without vacating it and dismissed the case. S.C. Coastal Conservation League v. Wheeler, No. 2:20-cv-03062 (D.S.C.).

July 1, 2021 EPA files a motions to remand the 2020 CWA Section 401 Certification Rule back to the agency without vacating the rule in the various ongoing cases. Del. Riverkeeper Network v. EPA, No. 2:20-CV-3412 (E.D. Pa.); In re Clean Water Act Rulemaking, No. 3:20-cv-04636 (N.D. Cal.); S.C. Coastal Conservation League v. Wheeler, No. 2:20-cv-03062 (D.S.C.).

May 27, 2021 EPA announces it intends to revisit the 2020 CWA Section 401 Certification Rule and schedules listening sessions throughout June 2021. It publishes its notice of intention in the Federal Register on June 2, 2021 outlining a number of questions on which it would like public comment.

May 11, 2021 Six states and the California State Water Resources Control Board write to the Army Corps of Engineers expressing concerns about the Corps’ reauthorization of nationwide permits based on the Trump administration’s revised regulations limiting state certification under Section 401 of the CWA.

Feb. 10, 2021 Court orders case held in abeyance for 60 days (until April 6, 2021). EPA is instructed to provide a status report by April 6, 2021. Del. Riverkeeper Network v. EPA, No. 2:20-CV-3412 (E.D. Pa.).

Jan. 22, 2021 Acting General Counsel for EPA, Melissa Hoffer, instructs DOJ to seek stays or abeyances in all ongoing litigation seeking review of any regulation promulgated during the Trump administration.

Jan. 20, 2021 President Biden instructs agencies to review all “existing regulations, orders, guidance documents, policies, and any other similar agency actions (agency actions)” for inconsistency with his statement of policy in Executive Order 13990, “Protecting Public Health and the Environment and Restoring Science To Tackle the Climate Crisis,” and consider suspending, revising, or rescinding these actions. The administration also releases a “List of Agency Actions for Review” that includes the 2020 Certification Rule.

Trump Administration I

Oct. 23, 2020 The Northern District of California consolidates American River v. Wheeler, California v. Wheeler, and Suquamish Tribe v. Wheeler. Proceedings will take place under In re Clean Water Act Rulemaking, No. 20-04636 (N.D. Cal.).

Aug. 31, 2020 The Suquamish and Pyramid Lake Paiute tribes and the Orutsararmiut Native Council file a lawsuit challenging the Clean Water Act Section 401 Certification Rule because the rule also affects tribal review and determinations under the CWA. Suquamish Tribe v. Wheeler, No. 3:20-cv-06137 (N.D. Cal.).

Aug. 26, 2020 A coalition of environmental and water conservation groups files a lawsuit challenging the Clean Water Act Section 401 Certification Rule. S.C. Coastal Conservation League v. Wheeler, No. 2:20-cv-03062 (D.S.C.).

July 21, 2020 A coalition of 20 states and the District of Columbia file a lawsuit challenging the Clean Water Act Section 401 Certification Rule. California v. Wheeler, No. 3:20-cv-04869 (N.D. Cal.).

July 13, 2020 The Delaware Riverkeeper Network files a lawsuit challenging the Clean Water Act Section 401 Certification Rule and alleges violations of the Administrative Procedure Act, Clean Water Act, and 10th Amendment. Del. Riverkeeper Network v. EPA, No. 2:20-CV-3412 (E.D. Pa.). American Rivers separately leads a coalition of national, regional, and state environmental groups in filing a lawsuit challenging the Rule, alleging violations of the Clean Water Act and Administrative Procedure Act. American Rivers v. Wheeler, No. 20-04636 (N.D. Cal.).

June 1, 2020 EPA finalizes the Clean Water Act Section 401 Certification Rule, limiting state authority over water quality certification. The final rule restricts the scope of the state review process to exclude consideration of “…air quality or transportation concerns, public access to waters, energy policy, or other multi-media or non-water quality impacts….” EPA is ambiguous on whether minimum flow can be considered under the rule, simply stating “…neither the proposed rule nor the final rule address minimum flow issues.” EPA also increases the stringency of the one-year deadline for state decisions by allowing the federal agency waiting on the state’s decision to set a “reasonable period of time” for the decision and giving that agency the power to determine whether the state has waived its right to make a decision.

Dec. 9-12, 2019 The Supreme Court declines to review the DC Circuit’s decision in Hoopa Valley Tribe v. FERC. FERC denies petitions for rehearing of its Aug. 2019 order filed by environmental organizations and an individual landowner and affirms its determination that New York waived its authority to issue or deny a water quality certification under section 401 for the Constitution Pipeline Project.

Aug. 28, 2019 The Federal Energy Regulatory Commission (FERC) issues an order determining that New York Department of Environmental Conservation waived its authority under section 401 to issue or deny a water quality certification for the Constitution Pipeline Project, based on the DC Circuit’s decision in Hoopa Valley Tribe v. FERC, No. 14-1271 (D.C. Cir.). The order also denied New York’s request for a stay, allowing the project to advance.

Aug. 26-Sept. 27, 2019 A coalition of environmental groups, led by California Trout and Trout Unlimited, petitions the Supreme Court to review the DC Circuit decision. Hoopa Valley Tribe v. FERC, No. 19-257 (2019). A coalition of 21 states, led by Oregon, files a brief as amici curiae in support of the petitioners.

Aug. 9, 2019 EPA proposes a regulation that would allow the agency to issue CWA permits over state objections concerning a project’s impact on climate change or air quality voiced through the section 401 certification process. This would prevent actions such as those taken in Washington, New York, and Oregon where state regulators used the section 401 certification process to block the construction of coal terminals, liquefied natural gas export facilities, and natural gas pipelines.

June 7, 2019 EPA releases guidance pursuant to section 3 of EO 13868 clarifying timelines for state review, the agency’s interpretation of the scope of review and the information that can be considered. This guidance provides insight into the administration’s more limited view of the scope of states’ section 401 certification authority.

April 10, 2019 President Trump issues EO 13868, the Executive Order on Promoting Energy Infrastructure and Economic Growth. Section 3 of the EO directs the EPA Administrator to review section 401 of the CWA and “EPA’s related regulations and guidance” to determine whether and how to adjust EPA regulations and guidance to ensure the efficient permitting of energy infrastructure. Once the Administrator has completed this review, he is directed to then issue new guidance and consider new regulations on section 401 permitting. For more information on section 3 of EO 13868, see Ari Sillman’s (JD ‘21) summary here.

Jan. 25, 2019 The DC Circuit rules that California and Oregon exceeded their authority under section 401 in the certification process for a set of hydroelectric dams on the Klamath River. Hoopa Valley Tribe v. FERC, No. 14-1271 (D.C. Cir.).

Aug. 16, 2018 The Senate Committee on Environment and Public works holds a legislative hearing entitled, “Hearing to Examine Implementation of Clean Water Section 401 and S. 3303, the Water Quality Certification Improvement Act of 2018.” The hearing centers on alleged state “abuses” of the section 401 water quality certification program.

G. W. Bush Administration

May 15, 2006 The Supreme Court affirms the ability of states to impose stricter discharge regulations through section 401 certification than the federal government requires in S. D. Warren Co. v. Me. Bd. of Envtl. Prot., 547 U.S. 370 (2006). The Court also reaffirms that regulations can include a minimum stream flow from hydroelectric dams to ensure minimal ecological disruption.

Clinton Administration

May 31, 1994 The Supreme Court expands scope of the section 401 certification process in PUD No. 1 v. Wash. Dep’t of Ecology, 511 U.S. 700 (1994) to include conditions for quantity of water flow. The Court holds that a state can require a minimum stream flow requirement as part of its section 401 certification process, refusing to create a distinction between water quality and quantity.