Shifting Power: The Supreme Court’s Decision in San Francisco v. EPA

The Supreme Court’s recent decision marks a pivotal moment in environmental law, potentially reshaping the balance of power between federal agencies and Congress, while setting new limits on the EPA’s regulatory reach.

On March 5, 2025, the Supreme Court of the United States ruled in City and County of San Francisco v. Environmental Protection Agency, holding that the EPA’s “end-result” permitting provisions exceeded its authority under the Clean Water Act. 

This article will explore the facts of the case, analyze the Court’s opinions, and discuss the potential long-term implications of the ruling.

FACTS OF THE CASE

Before examining the Court’s ruling, it is essential to understand how this case emerged.

San Francisco operates a combined sewer system, the only coastal city in California to do so. This system collects and treats both wastewater and stormwater runoff in the same network of pipes. However, during heavy rainfall, the system can exceed its capacity, leading to combined sewer overflows (CSOs) – discharges of untreated water, including pollutants, into the Pacific Ocean via the Oceanside Treatment Plant.

The Clean Water Act of 1972 (CWA) governs the discharge of pollutants into U.S. waters, granting the EPA authority to regulate such discharges. Under the National Pollutant Discharge Elimination System (NPDES) permit program, facilities must obtain permits that set limits on pollution discharges, monitoring and reporting requirements, and other conditions to safeguard water quality, aquatic life, and public health. Permittees are typically required to meet effluent standards – restrictions on pollutants discharged from point sources.

San Francisco has complied with the NPDES program for decades, implementing a CSO control plan since the late 1960s and completing construction of its North Point Wet Weather Plant in 1997. However, in 2019, the EPA and the California Regional Water Quality Control Board issued a new NPDES permit for the Oceanside facility with stricter conditions. Notably, this permit prohibited any discharge that contributes to a violation of applicable water quality standards in receiving waters – shifting compliance assessment from the point source (the facility itself) to the receiving body of water.

San Francisco objected, arguing that these provisions were inconsistent with the CWA and EPA regulations. City officials clarified that they were not challenging the EPA’s authority to regulate but rather sought clarity on the wastewater permit’s requirements to ensure compliance. The city specifically challenged two provisions in the permit: “the narrative prohibitions against violating water quality standards” and “a requirement that San Francisco update its long-term CSO control plan.” 

After the EPA’s Environmental Appeals Board rejected San Francisco’s administrative appeal in 2020, the city petitioned the U.S. Court of Appeals for the Ninth Circuit, which ruled in 2023 that the EPA’s permit conditions were authorized under the CWA and rationally connected to the administrative record.

San Francisco then petitioned the Supreme Court for review, and SCOTUS granted certiorari on May 28, 2024. Oral arguments took place on October 16, 2024, and the Court issued its decision on March 4, 2025.

The central question before the Court was: Does the Clean Water Act allow the Environmental Protection Agency (or an authorized state) to impose generic prohibitions in National Pollutant Discharge Elimination System permits that subject permit-holders to enforcement for violating water quality standards without identifying specific limits to which their discharges must conform?

OPINIONS OF THE COURT

In a 5-4 ruling, the Supreme Court held that “the Clean Water Act does not authorize the EPA to include ‘end-result’ provisions in wastewater discharge permits”. 

Justice Samuel Alito authored the majority opinion, joined by Chief Justice Roberts and Justices Gorsuch, Kavanaugh, and Thomas.The majority opinion examined the history of federal water pollution control and determined that the EPA’s end-result requirements contradict the regulatory framework Congress established under the CWA. 

Prior to 1972, the Water Pollution Control Act allowed enforcement actions against polluters based on the overall quality of the receiving waters. However, when Congress replaced that law with the CWA, it deliberately shifted to a model of imposing direct restrictions on polluters rather than retroactively assigning liability. The Court concluded that the EPA’s end-use requirements “would undo what Congress plainly sought to achieve when it scrapped the [Water Pollution Control Act] backward-looking approach.”

The majority, as the WilmerHale International Law Review noted, also identified two structural issues within the CWA that undermine the validity of end-result provisions:

1. The “Permit Shield” Provision – The CWA protects permit holders from liability if they comply with their permits. End-result provisions, which make permittees responsible for the final water quality regardless of compliance, would effectively strip permit holders of this protection.

2. The Lack of Mechanism for Allocating Responsibility Among Multiple Dischargers – The Court recognized that many bodies of water receive pollutants from dozens or even hundreds of sources, both permitted and unpermitted. Since the CWA does not provide a way to fairly assign responsibility among multiple dischargers, it is unreasonable to hold a single permit holder accountable for a water quality violation they may not have caused.

Additionally, the majority justified its ruling with two policy considerations: the elimination of end-use requirements would not harm businesses and municipalities; and the EPA possesses the expertise and resources to determine what specific actions a permit holder should take to protect water quality, rather than requiring cities and businesses to figure it out themselves.

Justice Amy Coney Barrett authored the dissenting opinion, joined by Justices Jackson, Kagan, and Sotomayor. The dissent took issue with the majority’s interpretation of the CWA, arguing that the statute explicitly directs the EPA to impose “any more stringent limitation” necessary to meet water quality standards. According to Barrett, the receiving water limitations in San Francisco’s permit fit squarely within this mandate.

The dissent also challenged the majority’s claim that end-result requirements mirror the pre-1972 enforcement model. Barrett argued that the real flaw of the old system was that it required unmanageable enforcement procedures after pollution had already occurred. The CWA addressed this issue by requiring permits before discharges occur – not by forbidding the EPA from considering water quality standards in permits altogether.

Finally, Barrett warned that eliminating end-result provisions could hinder the EPA’s ability to regulate water pollution efficiently. Without them, the EPA may need to delay or deny permits entirely if it cannot determine the precise steps necessary to meet water quality standards, potentially disrupting wastewater management and environmental protection efforts.

FUTURE IMPLICATIONS OF THE RULING

The Supreme Court’s ruling in San Francisco v. EPA has far-reaching consequences for the EPA’s regulatory authority, the administration of the CWA permitting system, and the broader landscape of administrative law. 

Many legal experts (e.g., WilmerHale International Law Review, Georgetown Environmental Law Review, Nossaman LLP) anticipate delays and complications in the EPA’s ability to issue permits under the new constraints. Previously, end-result requirements allowed flexibility for permittees to determine compliance methods. Now, the EPA must prescribe specific measures, which may require additional scientific assessments, increased staffing, and a more rigorous permitting process.

This challenge is compounded by the current administration’s efforts to reduce EPA staffing, potentially weakening the agency’s capacity to efficiently process NPDES permits. If the permitting process slows, it could disrupt municipal wastewater management, infrastructure projects, and industrial operations that depend on timely permit approvals.

Nossaman LLP notes that, while permit holders will benefit from clearer compliance expectations, the ruling raises significant questions about the EPA’s long-term ability to effectively administer the NPDES program and maintain water quality protections.

Beyond its impact on water quality regulation, this ruling aligns with the Supreme Court’s broader efforts to limit administrative agencies’ discretion. The decision comes at a pivotal moment as the Court recently overturned Chevron deference, the legal principle that previously required courts to defer to agency interpretations of ambiguous statutes. Without Chevron, agencies like the EPA will be forced to operate strictly within the text of the law, leaving less room for regulatory adaptation. 

The Court’s ruling reinforces the idea that if an agency finds an existing statutory framework inadequate, it must seek explicit authorization from Congress rather than expanding its own regulatory authority. This reassertion of congressional power over administrative rulemaking is a significant development in the ongoing debate over the role of federal agencies and the separation of powers. 

Jim Burling, Vice President of Litigation at the Pacific Legal Foundation, describes the ruling as a “demarcation of lines between congressional power, executive power, and judicial power.” 

By curbing the EPA’s ability to impose broad water quality conditions, the Court has effectively shifted authority away from administrative agencies and back to lawmakers. This raises the question of whether Congress will take action to amend the CWA and grant the EPA clearer authority to regulate water pollution under a more structured framework. However, given the political divide on environmental regulation, such legislative action remains uncertain.

Ultimately, San Francisco v. EPA is not just a case about water quality permits – it is a landmark decision reshaping the balance of power between federal agencies, Congress, and the courts. While the ruling provides clarity for permit holders, it also limits the EPA’s flexibility in addressing pollution. This raises questions about how the agency will adapt to its new constraints. Whether through congressional action or alternative regulatory strategies, the long-term effects of this ruling will shape the future of environmental governance for years to come.