ENVIRONMENTAL REGULATION SERIES
The Death of Chevron Deference: The U.S. Supreme Court Does Away With End-Result Permit Requirements
A first look at the Court’s decisive roll-back of agency authority and shifting the burden to the EPA to articulate limitations rather than results.
On March 4, 2025, the United States Supreme Court issued its first major environmental law decision since it overruled the Chevron doctrine in June 2024, upending decades of environmental law decisions premised on agency deference in the face of statutory ambiguity.[1] In a 5-4 opinion by Justice Alito, the Supreme Court held that the EPA exceeded its authority under the Clean Water Act (CWA) when it included two “end-result” permit requirements in a wastewater treatment facility discharge permit for the City of San Francisco. City & Cnty. of San Francisco, California v. Env’t Prot. Agency, No. 23-753, 2025 WL 676441, at *3 (U.S. Mar. 4, 2025). The first requirement prohibits the facility from making discharges that “contribute to a violation of any applicable water quality standard” for receiving waters, and the second provides that the facility cannot perform any treatment or make any discharge that “create[s] pollution, contamination, or nuisance as defined by California Water Code section 13050.” Id. at *5.
The Court rejected San Francisco’s broad argument that all limitations under §1311 must qualify as effluent limitations and noted that the text of §1311 and related statutes authorize EPA to impose effluent or other limitations.[2] The Court reasoned that under the principles of statutory interpretation, when “Congress includes particular language in one section of a statute but omits it in another section of the same Act, it is generally presumed that Congress acts intentionally and purposely in the disparate inclusion or exclusion.” City of San Francisco, 2025 WL 676441, at *5.
Accordingly, permit limitations may be effluent limitations or other limitations not necessarily quantitative in nature. Effluent limitations [3] can include technology-based limitations,[4] which require the use of specified pollution treatment technologies, or water quality based effluent limitations (WQBELs),[5] which require discharges be made without unduly impairing water quality regardless of cost or available technology. Other limitations can include narrative provisions requiring the permit holder to do non-quantitative things like following “best practices.”[6]
The Court then addressed San Francisco’s second, more narrow argument: that the EPA is not authorized “to impose NPDES permit requirements that condition permitholders’ compliance on whether receiving waters meet applicable water quality standards.” City of San Francisco, 2025 WL 676441, at *7. The Court agreed.
First, the text of 33 USC §1311(b)(1)(C) requires a permit to contain two types of limitations: effluent limitations and “any more stringent limitation[s]” required to meet water quality standards. Id. However, when setting limitations, the EPA must set rules for a permit holder to follow to achieve the desired result (e.g. a degree of water quality), not merely state the desired result and leave it up to the permittee to figure out what it must do to achieve that result. Id.
Section 1311(b)(1)(C) tells the EPA to impose requirements to “implement” water quality standards—that is, to “ensure” “by concrete measures” that they are “actual[ly]” “fulfill[ed].” Simply telling a permittee to ensure that the end result is reached is not a “concrete plan” for achieving the desired result. Such a directive simply states the desired result; it does not implement that result.
City of San Francisco, 2025 WL 676441, at *8. Thus, a permit limitation is not synonymous with the standard it seeks to achieve, and it is EPA’s job to set out actions that must be taken to achieve the objective of a certain degree of water quality.
Second, the Court pointed to the legislative history of the CWA and noted that prior to 1972, the Water Pollution Control Act (WPCA) explicitly provided that a permittee could be liable if the quality of the water into which it discharged pollutants failed to meet water quality standards. Id. at *8. When the statute was overhauled in 1972, Congress purposefully and deliberately left out a comparable provision in the CWA. The revision was aimed to facilitate enforcement by making it unnecessary to work backwards from the pollution to determine the responsible source, and instead “to achieve acceptable quality standards by means of direct restrictions on polluters.” Id. at *9. EPA’s interpretation, which effectively reads back into the law the deleted provision, is contrary to the legislative intent of the CWA.
Third, the Court considered the context of §1311 in view of the broader statutory scheme and identified two key features that support its interpretation: first, the importance of the “permit shield provision”[7] in light of the extreme penal nature of the CWA, and second, the lack of a provision addressing the situation where more than one permittee is discharging into water of substandard quality. The CWA imposes a liability scheme of strict civil liability in addition to heavy penalties for violations of water quality standards, not to mention the possibility of criminal prosecution for knowing or negligent actions. Accordingly, the permit shield provision, which protects a permittee from penalties if it follows the terms in its permit, is critical. The Court reasoned that
the benefit of [the permit shield] provision would be eviscerated if the EPA could impose a permit provision making the permittee responsible for any drop in water quality below the accepted standard. A permittee could do everything required by all the other permit terms. It could devise a careful plan for protecting water quality, and it could diligently implement that plan. But if, in the end, the quality of the water in its receiving waters dropped below the applicable water quality levels, it would face dire potential consequences. It is therefore exceedingly hard to reconcile the Government’s interpretation of § 1311(b)(1)(C) with the permit shield.
City of San Francisco, 2025 WL 676441, at *10. The Court also pointed to the absence of any provision addressing the problem of multiple dischargers into the same substandard body of water under the CWA. Given that Congress repealed the enforcement scheme of the WPCA which penalized dischargers for a drop in water quality standards of the body of water to which it was discharging, the Court was not convinced that § 1311(b)(1)(C) was intended to perpetuate that enforcement scheme in the absence of any provision addressing the multi-discharger problem.[8]
Ultimately, this decision spells the end of end-result requirements in discharge permits under the CWA, and the Court’s reasoning will inform future environmental law decisions touching on the agency’s role in permitting.
[1] See Loper Bright Enterprises v. Raimondo, 603 U.S. 369, 144 S. Ct. 2244, 219 L. Ed. 2d 832 (2024) (overruling Chevron, U.S.A., Inc. v. Natural Resources Defense Council, Inc., 467 U.S. 837, 104 S. Ct. 2778, 81 L. Ed. 2d 694 (1984)).
[2] See § 1341(d) (referring to “effluent limitations and other limitations, under section 1311”); § 1365(f ) (referring to “effluent limitation[s] or other limitation[s] under section 1311”); § 1367(d) (same); National Assn. of Mfrs. v. Department of Defense, 583 U. S. 109, 122 (2018) (interpreting the phrase “effluent limitation or other limitation” in the CWA’s judicial review provision, § 1369, to encompass both “effluent” limitations and limitations such as “non-numerical operational practice[s]” and “equipment specification[s]”).
[3] Effluent limitations are defined as restrictions on the “quantities, rates, and concentrations of chemical, physical, biological, and other constituents.”33 USC § 1362(11).
[4] 33 U.S.C. §1311(b)(1)(A) and (B) (requiring “best practicable control technology” and for publicly owned treatment works “pretreatment” or “secondary treatment”).
[5] 33 U.S.C. §1311(b)(1)(C)(requiring “any more stringent limitation, including those necessary to meet water quality standards, treatment standards, or schedules of compliance, established pursuant to any State law or regulations . . . or any other Federal law or regulation, or required to implement any applicable water quality standard established pursuant to this chapter.”).
[6] See Id.
[7]33 U. S. C. § 1342(k), under which a permittee is deemed to be in compliance with the CWA if it follows all the terms in its permit.
[8] Under the WPCA scheme, the EPA had to “unscramble the polluted eggs after the fact,” which was impractical. Id. at *10.
