SCOTUS Rolls Back EPA’s Permitting Authority under the CWA

March 7, 2025

On March 4, 2025, the United States Supreme Court issued its ruling in City and County of San Francisco v. Environmental Protection Agency, limiting the U.S. Environmental Protection Agency (EPA)’s permitting authority under the Clean Water Act (CWA).

The case centered on the scope of the National Pollutant Discharge Elimination System (NPDES), a key component of the CWA that prohibits pollutant discharges into regulated waters without a permit. San Francisco contested the EPA’s authority to impose “end-result” conditions in its NPDES permit. Specifically, the challenged provisions barred the City from: (1) discharging pollutants in a manner that contributes to a violation of water quality standards in receiving waters; and (2) conducting treatment or discharges that create pollution, contamination, or nuisance under California law.

The Supreme Court ruled that the CWA does not empower the EPA to impose NPDES permit conditions that make compliance contingent on whether receiving waters meet applicable water quality standards. As a result, the Court struck down the two contested provisions.

Here are the key takeaways:

1. Increased Transparency and Predictability in NPDES Permitting: The ruling mandates the inclusion of specific, enforceable limitations within NPDES permits, thereby eliminating the reliance on ambiguous “end-result” provisions and affording permittees enhanced clarity regarding their CWA obligations.
2. Reinforcement of the Permit Shield Doctrine: The decision reaffirms the statutory protection afforded to permittees who comply with the express terms of their NPDES permits, shielding them from civil and criminal liability under the CWA.
3. Equitable Allocation of Responsibility for Water Quality Impairments: The ruling mitigates the potential for permittees to be held liable for water quality impairments attributable to extraneous sources of pollution, acknowledging the complex interplay of multiple discharges into a given waterbody.
4. Recommended Review of Existing NPDES Permits: Entities holding NPDES permits are advised to conduct a thorough review of their permits to identify any provisions inconsistent with the ruling, specifically “end-result” based limitations.

Going forward, this means that CWA permit terms can specify numeric limits on discharges and may also provide steps the discharger must take to reduce pollution (such as testing and reporting), but they may not impose restrictions based on water quality alone.

For consultation on the implications of this decision for your operations, permitting, or planned projects, please contact McGlinchey’s Environmental practice.