Water Quality and Wetlands Committee Report

I. Judicial

A. CWA Section 303 – Water Quality Standards (WQS)

In Grand Portage Band v. EPA two Bands of Lake Superior Chippewa challenged the Environmental Protection Agency’s (EPA) approval of Minnesota’s revised water quality standards for industrial and agricultural uses, which replaced numeric criteria for certain pollutants with narrative criteria. The Bands argued that the EPA’s approval was arbitrary and capricious because it failed to consider the impact of the revisions on aquatic life, wild rice, and the Bands’ treaty-reserved rights to use Minnesota waters. Although the court chastised EPA for its lack of meaningful consultation with the Bands, it denied the Bands’ motion for summary judgment and granted the motions for summary judgment from the EPA and intervenor-defendants. Relying in part on deference given to agencies in areas of their expertise, the Court found that EPA’s approval was not unreasonable and that the existing water quality standards for aquatic life and wild rice remained in effect to protect those uses.

In Association of Washington Business v. EPA, a group of Washington business associations, including the Northwest Pulp & Paper Association and the American Forest & Paper Association, challenged a 2022 EPA rule that imposed federal water-quality standards on Washington State. The controversy centers on the EPA’s decision to reimpose federal human health criteria for water quality, particularly concerning polychlorinated biphenyls, which the EPA deems necessary to protect subsistence fishers, including tribal members with treaty-reserved fishing rights. The plaintiffs argue that the EPA’s rule reverses previous policy without adequate justification and improperly relies on tribal treaty rights. The court denied the EPA’s motion to transfer the case to the Western District of Washington and granted motions for intervention by the State of Washington and several tribes, highlighting the significant involvement of D.C.-based officials in the rule’s promulgation and the potential national implications of the decision.

B. CWA Section 309 – Enforcement

In United States v. Denali Water Solutions, LLC, EPA entered into a consent decree with Denali Water Solutions, LLC (Denali), a company headquartered in Russellville, Arkansas that accepts, hauls, and land applies biosolids generated by municipal wastewater treatment systems nationwide. The consent decree resolved allegations that Denali violated Section 405(e) of the Clean Water Act by disposing of sewage sludge from publicly owned treat works at hundreds of land application sites in California and Arizona in violation of biosolids regulations. The settlement requires Denali to pay a $610,000 civil penalty and to implement a “Soil Sampling and Agronomic Rate Calculation Protocol” (Protocol) if it does business in Arizona or California in the next five years. The Protocol is the first of its kind and is intended to set an industry standard to ensure that biosolids are applied at or below the agronomic rate for each land application site.

In United States v. Guam Waterworks Authority, EPA entered into a consent decree with Guam Waterworks Authority (GWA) and the government of Guam resolving allegations that GWA violated the Clean Water Act and terms and conditions of its National Pollutant Discharge Elimination System permits by exceeding effluent limits, failing to prevent sanitary sewer overflows, and failing to properly operate and maintain its systems at the four wastewater treatment systems it operates on Guam. The settlement requires GWA to conduct a comprehensive assessment of its sanitary sewer system to identify defective sewer pipes and gravity mains in poor condition and to upgrade its collection system to address sanitary sewer overflows to the Pacific Ocean. The total cost of implementing these and other required measures is estimated to be approximately $400 million over the ten-year period to complete the injunctive relief. GWA will also submit a plan to upgrade its Agana/Hagatna wastewater treatment plant to secondary treatment, implementation of which will be required in a subsequent consent decree.

C. CWA Section 401 – Water Quality Certification

In In re: Clean Water Act Rulemaking, the U.S. District Court for the Northern District of California dismissed as moot a challenge that twenty states, a handful of environmental groups, and tribes brought against the Trump administration’s change to the Section 401 certification rule issued in 2020. The rule change curtailed states’ and tribes’ authority to challenge federal infrastructure projects. The Biden administration replaced the Section 401 certification rule in late 2023. Following the Biden administration’s issuance of the 2023 rule, a different group of states sued in federal court challenging the validity of the rule. These states have argued that the 2023 rule grants states too much authority to undermine projects under the CWA by broadening the scope of Section 401 certification review to include the entire activity proposed by the project applicant rather than confining review to the proposed discharge in the application. Several other states have intervened in support of the rule. The Louisiana district court denied the states’ request for a preliminary injunction blocking the new rule. At the time of writing, the matter is being held in abeyance to allow time for the incoming administration to determine how they will proceed, and the court has not yet ruled on motions for summary judgment filed by the parties.

In Sierra Club v. Tennessee Department of Environment & Conservation, the Sixth Circuit granted environmental groups’ requested stay of a Section 401 certification and a Section 404 permit for a Tennessee Valley Authority pipeline construction project on the grounds that Tennessee and the U.S. Army Corps of Engineers failed to consider less impactful alternatives for the project’s water crossings. Judge Thapar dissented, writing that the federal court lacked subject matter jurisdiction because the petitioners’ claims arose under the state administrative procedure act (APA), even though the state’s resulting order provided Section 401 certification for the project. According to the dissent, the CWA (specifically, 33 U.S.C. § 1365(a)(1), among other authorities including the federal APA) does not provide a cause of action for such claims.

D. CWA Section 402 – National Pollutant Discharge Elimination System (NPDES)

In Center for Biological Diversity v. Regan, the D.C. District Court upheld its order vacating Florida’s authority to administer CWA Section 404 permits. The district court previously reversed EPA’s grant of CWA permitting authority (including Section 402 discharge permits) to the state of Florida. Florida moved to stay the order, but the district court denied the request, finding that Florida failed to prove the requirements for a stay. Because the U.S. Army Corps of Engineers was both willing and capable to take over the administration of the permitting program, Florida could not demonstrate that it was likely to suffer irreparable harm if the stay was not granted. While Florida argued that a continuing stay would damage its sovereign interests in conservation and authority to enforce existing permits, the district court disagreed, reiterating that the CWA was a federal statute protecting navigable waters of the United States and that Florida was still free to enforce state law and uphold previously issued permits.

In Stone v. High Mountain Mining Company, the U.S. Court of Appeals for the Tenth Circuit held that indirect discharges into unlined ponds may require a NPDES permit based on the seven factors outlined in the U.S. Supreme Court’s decision in County of Maui v. Hawaii Wildlife Fund. Here, the defendants discharged mining operation wastewater into unlined settling ponds. The plaintiffs argued that a NPDES permit was required because pollutants seeped through the unlined ponds into the South Platte River through groundwater in a manner equivalent to a direct discharge. The district court concluded that the discharges were functionally equivalent to direct discharges, primarily because three of the seven Maui factors—transit time, distance traveled, and nature of the material passed through—were met. However, the district court explicitly disregarded the remaining four factors due to a lack of evidence. The Tenth Circuit reversed and remanded the decision, emphasizing that while the factors considered by the district court were important, they were not dispositive and other factors, such as dilution and amount of discharge, might be important, such that analysis of additional Maui factors is necessary.

Coastal Environmental Rights Foundation v. Naples Restaurant Group, LLC involved a citizen’s suit where the plaintiff sought civil penalties and an injunction to prevent the defendants from discharging pollutants without a NPDES permit by launching fireworks off a barge during their annual Fourth of July show. The trial court held that proof of a single instance of a firework falling into the bay without a permit was insufficient to prove an ongoing violation of the CWA. Regardless, shortly after the trial court decision, the defendants obtained a NPDES permit authorizing the discharges. The question on appeal was whether the claims for both civil penalties and injunctive relief became moot when the defendant obtained a NPDES permit. The Ninth Circuit addressed a circuit court split. Under the Eight Circuit’s minority view, claims for civil penalties and requests for injunctive relief are both moot when it is “absolutely clear that the allegedly wrongful behavior could not reasonably be expected to recur.” By contrast, the majority position holds that a finding of mootness for injunctive relief does not automatically moot a request for civil penalties. The Ninth Circuit embraced the minority view, concluding that the violation was not reasonably expected to recur due to the defendants’ acquisition of the NPDES permit, rendering both the injunction and civil penalties claims moot. The court vacated the district court’s ruling and remanded with instructions to dismiss the case as moot.

In Puget Soundkeeper Alliance. v. Port of Tacoma, the Ninth Circuit Court of Appeals held that the citizen-provision of the CWA, section 505, authorizes citizens to enforce in federal court any condition of a state-issued pollutant-discharge permit, even those adopted under state-law authority that mandate “a greater scope of coverage than” the CWA. In Port of Tacoma, the defendants owned and operated a marine cargo terminal subject to Washington State’s Industrial Stormwater General Permits (ISGP). “The Wharf” is an overwater portion of that terminal used solely for loading and unloading cargo containers. Because the Wharf does not receive discharges from portions of the Terminal defined by EPA as being “associated with industrial activity,” discharges from the Wharf are exempted from federal industrial-stormwater requirements. The issues were whether Washington’s ISGP nonetheless covered discharges from the Wharf, and, if it did, whether a citizen could enforce such conditions in federal court under the CWA’s citizen-suit provision. The district court determined that the ISGP did not cover the entire footprint of industrial facilities and thus did not cover discharges from the Wharf. The Ninth Circuit reversed, holding that areas like the Wharf must meet the ISGP’s requirements. The court further held that citizens can enforce in federal court all conditions of state-issued pollutant-discharge permits, even those that “prescribe a greater scope of coverage than the federal regulations.”

On October 16, 2024, the U.S. Supreme Court heard oral arguments in City and County of San Francisco v. EPA, The case addresses whether the EPA can impose generic, narrative prohibitions in NPDES permits and enforce violations of water quality standards without identifying specific discharge limits. The Ninth Circuit upheld the EPA’s prohibitions in 2023. During oral argument, the justices focused on whether the statute’s language captures generic prohibitions against violating standards, particularly the provision that allows for “any more stringent limitation” necessary to meet water quality standards. In addition, Justices Roberts and Gorsuch expressed concerns related to fairness and the potential for arbitrary enforcement, while Justices Kagan and Sotomayor emphasized Congress’ intent in creating a statutory scheme that allowed the EPA the flexibility to address evolving water quality challenges.

On March 4, 2025, the U.S. Supreme Court issued its decision in City and County of San Francisco v. EPA. The opinion, authored by Justice Alito, addressed whether the EPA can enforce “end-result” requirements in NPDES permits. According to the Court, “end-result” requirements are permit provisions “that do not spell out what a permittee must do or refrain from doing but instead make a permittee responsible” for water quality violations in receiving water bodies. The U.S. Supreme Court reversed the Ninth Circuit’s judgment, holding that while the Clean Water Act authorizes the inclusion of narrative criteria in NPDES permits, the Act does not authorize “end-result” requirements. The Court emphasized that EPA has the tools and responsibility to determine the steps a permittee must take to ensure water quality standards are met.

E. CWA Section 404 – Wetlands, including Waters of the United States (WOTUS)

In Lewis v. United States, the Court addressed whether wetlands on the Lewis property qualified as “waters of the United States” under the CWA. After seven site visits, the U.S. Army Corps of Engineers (the Corps) determined in 2016 that portions of the property contained wetlands subject to CWA jurisdiction. Following appeals and administrative reconsideration, the Corps issued an Approved Jurisdictional Determination (AJD) in 2017, which Lewis challenged in federal Court as arbitrary and capricious under the APA. The District Court found the administrative record insufficient to support the Corps’ conclusion that the wetlands met the “adjacency” test or had a “significant nexus” to traditional navigable waters and remanded the case for further review. On remand, the Corps issued a 2020 AJD under the Navigable Waters Protection Rule, which significantly revised its findings but was later withdrawn after Lewis filed a second lawsuit. On appeal, the Fifth Circuit found that photographs and other evidence demonstrated no continuous surface connection between the wetland and a relatively permanent body of water, as required by the Supreme Court’s ruling in Sackett v. EPA to qualify as WOTUS. The nearest body of water was miles away, separated by roadside ditches, a culvert, and non-permanent tributaries. The Fifth Circuit vacated the District Court’s judgment and remanded with instructions to enter judgment in favor of Lewis, concluding that the tracts in question were not WOTUS.

In Glynn Environmental Coalition, Inc. v. Sea Island Acquisition, the defendant had obtained authorization from the Corps in 2013 to fill 0.49 acres of land for a development project under Nationwide Permit 39. Plaintiffs filed a citizen suit in 2019, alleging the property contained jurisdictional wetlands. The Court retroactively applied the Sackett test, under which wetlands must have a continuous surface connection to a traditional navigable water to qualify as WOTUS. Plaintiffs argued that water from the property flowed to an adjacent salt marsh and Dunbar Creek via surface runoff, groundwater, and culverts. However, photographic evidence and descriptions showed a “clear demarcation” between the property and Dunbar Creek, with intervening upland areas, roads, and a salt marsh separating them. The Court held that the plaintiffs failed to demonstrate the continuous surface connection required by Sackett and dismissed the case.

In Inland Empire Waterkeeper v. Corona Clay Co., the plaintiff alleged that the defendant’s industrial facility discharged stormwater into Temescal Creek, which eventually flows into the Pacific Ocean, and argued that Temescal Creek was a WOTUS under the plurality rule in Rapanos v. United States. Plaintiff contended that Temescal Creek is a natural surface waterbody with a direct connection to the Santa Ana River, and supported this claim with evidence that Temescal Creek remains a geographic constant, including aerial photos, streamflow gages showing consistent flow even in dry months, and expert observations of water in the creek during a June 2022 site visit. After a jury trial found in favor of Plaintiff, the defendant moved for a new trial, arguing that the Sackett decision changed the law on what constitutes a WOTUS and that the plaintiffs’ counsel made improper arguments during closing. The Court found that Sackett did not alter the prevailing law applicable to the case and upheld the jury’s verdict because plaintiffs had demonstrated Temescal Creek is a tributary with a direct surface connection to the Santa Ana River and, therefore, a WOTUS subject to CWA jurisdiction under both Rapanos and Sackett.

In United States v. Sharfi, the Court applied the Sackett test to determine whether wetlands on the Defendants’ property qualified as WOTUS under CWA. The parties agreed that Bessey Creek, located 4.5 miles from the site, is a relatively permanent water that eventually flows into the St. Lucie River, the St. Lucie Inlet, and the Atlantic Ocean, all of which are traditional navigable waters. However, they disputed whether three manmade ditches near the site constituted WOTUS. The Plaintiff argued that the wetlands physically abutted these ditches, which allegedly had a relatively permanent flow to navigable waters. The Court, however, found that the ditches were manmade drainage channels, not natural water features, and lacked the continuous flow required to qualify as WOTUS under Sackett. The Court further noted that the ditches were characterized by straight-line construction, discontinuous berms that impeded surface flow, and seasonal rather than continuous water flow. These characteristics did not meet the Sackett standard of a “relatively permanent, standing or continuously flowing body of water.” Consequently, the Court held that the wetlands on the defendants’ property were not adjacent to any regulated WOTUS, failing the first prong of the Sackett test, and granted summary judgment in favor of the defendants.

In United States v. Valentine, the Court addressed whether wetlands on the Defendant’s property fell within the jurisdiction of the CWA under the Sackett standard. The Defendants developed a hunting club on their 1,700-acre property in North Carolina, which is located within a floodplain of wetlands adjacent to Devils Gut, Gardner Creek, and the Roanoke River—all WOTUS. Defendant constructed roads, dikes, and a lodge building using fill material extracted from borrow pits within the wetlands, altering natural water flow, creating standing water, and causing sedimentation in surrounding wetlands without obtaining a permit. The United States argued that a continuous surface connection existed between the affected wetlands and Devils Gut, Gardner Creek, and the Roanoke River, thereby meeting the Sackett test for adjacency. Defendant contested this claim, asserting that the government failed to demonstrate practical indistinguishability between the wetlands and navigable waters and argued that continuous surface connection and practical indistinguishability are separate jurisdictional requirements.

The Court rejected Defendant’s arguments, clarifying that Rapanos and Sackett established a continuous surface connection as the defining characteristic of practical indistinguishability. The Court found that the government had plausibly alleged jurisdiction under the CWA, noting that the wetlands’ adjacency to traditional navigable waters was sufficient to invoke the Act’s protections. Additionally, the Court dismissed the Defendant’s argument that floodwaters undermine the notion of a continuous surface connection, emphasizing that adjacency does not require flooding to establish jurisdiction. Ultimately, the Court held that the government’s allegations were sufficient to support jurisdiction under the CWA.

In United States v. Sweeney, the Court held that wetlands and tidal waters on Point Buckler Island in the San Francisco Bay Delta remained within CWA jurisdiction under the Sackett test. The government demonstrated that the wetlands directly abutted tidal waters, including Suisun Bay and Grizzly Bay, and had a continuous surface connection, making them indistinguishable from the tidal waters. The Defendants argued that man-made barriers, such as a levee they constructed, precluded jurisdiction, but the Court rejected this argument, noting that temporary or artificial separations do not remove wetlands from CWA protection. The Court found that the Defendants illegally discharged pollutants into tidal waters and wetlands without a permit, violating the CWA. The Court denied Defendants’ motion for relief, affirming that Sackett did not alter its prior judgment.

In Orutsararmiut Native Council v. United States Army Corps of Engineers, the Court examined the application of CWA Section 404 to Donlin Gold’s proposed mine project. The project involved the discharge of approximately 21,774 cubic yards of fill material into the Kuskokwim River to construct a port near Jungjuk Creek, impacting wetlands and aquatic ecosystems. Under Section 404, the Corps is required to determine whether such discharges would result in “significant degradation” of WOTUS, considering factors such as human health and welfare, aquatic ecosystem diversity, and recreational, aesthetic, and economic values. Plaintiffs challenged the Corps’ conclusion that the project would not cause significant degradation, arguing that the agency improperly relied on mitigation measures, including monitoring programs and advisory committees. The Court also addressed the Plaintiffs’ contention that barge activity associated with the project should have been considered a secondary effect of the fill discharge. Under Section 404, secondary effects are those indirectly caused by the fill activity, such as water level changes or leaching from the fill material. Plaintiffs argued that the barge traffic supporting the mine’s operations would significantly impact wetlands and aquatic ecosystems, particularly subsistence fisheries in the Kuskokwim River. The Court, however, found that barge activity was not a secondary effect of the fill discharge as it did not arise directly from the discharge itself. The Court upheld the Corps’ decision, concluding that the agency properly limited its analysis to the direct effects of the fill discharge and reasonably determined that the project would not result in significant degradation of wetlands and aquatic ecosystems.

In White v. U.S. Army Corps of Engineers, the Plaintiff challenged the Amended Rule issued by the Corps and the EPA in 2023, which revised the definition of WOTUS under the CWA. The lawsuit, filed under the APA, alleged that the rule’s provision for adjacent wetlands was inconsistent with the Supreme Court’s test in Sackett v. EPA. The Sackett decision established that wetlands qualify as jurisdictional waters if they (1) are adjacent to a relatively permanent body of water, and (2) have a continuous surface connection to that water, making it difficult to determine where the water ends and the wetland begins. The Amended Rule adopted this standard by defining adjacent wetlands as those with a continuous surface connection to jurisdictional waters. The Plaintiff argued that Sackett requires wetlands to meet a second, independent test of being “practically indistinguishable” from jurisdictional waters, in addition to having a continuous surface connection. The Court rejected this argument, clarifying that Sackett treats a continuous surface connection as sufficient to establish indistinguishability. Wetlands separated by barriers or lacking such a connection are excluded from federal jurisdiction under both Sackett and the Amended Rule. This decision affirms that the Amended Rule aligns with Sackett and limits federal jurisdiction to wetlands meeting the continuous surface connection standard and rejecting attempts to impose additional criteria.

F. CWA Section 505 – Citizens Suits

In Mid-New York Environmental and Sustainability Promotion Committee, Inc. v. Dragon Springs Buddhist, Inc., plaintiffs were in court a second time alleging that the defendant was discharging stormwater in violation of its NPDES and Construction permits. The court granted defendant’s Motion to Dismiss due to absence of notice because the plaintiff’s Notice of Intent (NOI) lacked sufficient information to enable the defendant to identify and cure its alleged violations. The NOI, while alleging that discharges violated an effluent limitation, did not actually allege illegal groundwater discharges or that those discharges found their way to surface water. The NOI also failed to identify a point source as required by the CWA. While the term “point source” is to be broadly interpreted, the NOI at issue in this case described a “steep slope” on the northeast side of defendant’s property and “the area southwest of the bridge.” The court noted that this description identifies areas of land marked by certain features, but it did not identify a “discernible, confined, and discrete conveyance.”

StarLink Logistics, Inc. v. ACC, LLC involved claims arising both before and after the issuance of a state-issued consent order that addressed the defendant’s discharge from a landfill without a NPDES permit as required by the CWA. Plaintiffs filed a citizen suit alleging that, both before and after the consent order, contaminated water from the defendant’s landfill flowed to the plaintiffs’ property without a NPDES permit. The trial court disposed of the pre-consent order claims as moot or, in the alternative, precluded by the consent order. It dismissed the post-consent order claims for lack of notice. The Sixth Circuit Court of Appeals affirmed the dismissal of certain pre-consent order claims on the basis of claim preclusion, as the consent order addressed the same permitting issues. The Sixth Circuit agreed with the plaintiffs that the post-consent order claims were not precluded by the consent order because they could not have been addressed in the former suit. However, the post-consent order claims were ultimately dismissed for failure to provide proper notice. The Sixth Circuit held that issuance of a consent decree alters a plaintiff’s CWA notice obligations, requiring a new round of notice for post-consent order violations. Here, while the plaintiffs provided the initial 60-day required notice, they did not provide additional notice after the state issued a consent order, leading to the dismissal of claims related to NPDES permitting violations.

In South River Watershed Alliance, Inc. v. City of Atlanta and Atlanta Police Foundation, Inc., the U.S. District Court for the Northern District of Georgia denied the plaintiff’s Motion for Preliminary Injunction to halt defendants’ construction of a law enforcement facility near an impaired body of water. The plaintiff alleged that defendants’ construction activities discharged sediments into the creek in violation of a General Permit issued by the state for stand-alone construction projects disturbing an acre or more. The defendant argued that the court lacked subject matter jurisdiction because: (1) the violations alleged by defendant were “not supported by law” such that the plaintiff had not demonstrated an “ongoing violation” of the CWA as required by Gwaltney; and (2) the plaintiff had failed to comply with the pre-suit notice requirement. The court rejected both arguments. With respect to the first, the court found that defendant’s contention was actually a question of whether there was a violation of the CWA at all – a key issue on the merits – and not a question of whether the violation is ongoing. With respect to the second, there is a circuit split as to whether pre-suit notice requirement is a jurisdictional issue. Here, the court did not view the defendant’s arguments regarding pre-suit notice as a challenge to the court’s subject matter jurisdiction under Federal Rule of Civil Procedure 12(b)(1). The court also agreed with the plaintiff that violations of Georgia’s water quality standards may, on their own, form the basis of a CWA citizen suit, as discharges that violate the state’s water quality standards are a violation of the General Permit.

In Snake River Waterkeeper v. J.R. Simplot Co., the plaintiff environmental group sued the owner and operator of a large Confined Animal Feeding Operation (CAFO) alleging it was discharging manure into the Snake River without a NPDES permit. The defendant filed a Motion to Dismiss for lack of subject matter jurisdiction, arguing that plaintiff’s NOI failed to allege facts sufficient to describe exactly where, when, and how such discharges were occurring, or to demonstrate ongoing violations. The court denied defendant’s Motion, noting numerous pieces of evidence that were provided to Defendant in the NOI, including: (1) aerial photographs; (2) citations to Defendant’s comments to EPA concerning issuance of the general permit for CAFOs in Idaho; (3) a map of the parcel ownership; (4) testing results and locations; (5) identifying specific parcel numbers of the land at issue; and (6) a flow map of tributaries running through Defendant’s facility to the water body at issue. The court explained that a notice must be reasonably specific when identifying the location, nature and time of the alleged violation but is not required to identify specific discharge points. The court specifically drew attention to the fact that a plaintiff is not required to identify the specific date of an alleged violation—a violation is premised on the alleged violator’s failure to act, which is different from challenging specific instances of discharge. The court also noted that the Gwaltney requirement that a plaintiff establish an ongoing violation applies to complaints and not to notice letters.

In Save the Cutoff v. Iron River Ranch II, LLC, the court granted defendant’s motion to dismiss for lack of subject matter jurisdiction. Plaintiff, a non-profit organization, alleged that the defendants, a property owner and a construction company, illegally placed fill material in Cedar Creek, a tributary of the Trinity River, without a permit. The plaintiff alleged that the defendants deposited fill material one time and that this constituted a continuing violation because the fill remained in Cedar Creek and continued to be discharged due to its placement. The defendants argued the one-time placement of fill constituted a wholly past discharge that was not ongoing. The court agreed with the defendant, but indicated it might have ruled differently had the plaintiff alleged that the defendants continued to place fill or were reasonably likely to continue doing so. The court provided a number of examples from other cases of activities that are not ongoing discharges, including migration, decomposition or dissolution of contamination from previous releases, and distinguished cases holding that the stormwater runoff from fill material may be a continuing violation where the runoff originated from material “outside” Waters of the United States, as opposed to here, where the runoff was already present in the Waters.

II. Legislative and Rulemaking

A. CWA Section 303 – Water Quality Standards (WQS)

On May 2, 2024, EPA published a final rule revising the CWA WQS regulation at 40 C.F.R. Part 131 to explicitly address how the EPA and states must consider Tribal reserved rights – defined in this rule as “rights to CWA-protected aquatic and/or aquatic-dependent resources reserved to Tribes through treaties, statutes, or executive orders” – in establishing water quality standards, where Tribes assert these rights for consideration. The rule creates a regulatory framework to be applied consistently while accounting for local conditions and factors to inform the development of water quality standards to protect applicable Tribal reserved rights. The rule requires that if a Tribe asserts a Tribal reserved right in writing to a state and EPA for consideration in establishment of WQS, the state must, to the extent supported by available data and information: 1) take into consideration the use and value of its waters for protecting the Tribal reserved right in adopting or revising designated uses; 2) take into consideration the anticipated future exercise of the Tribal reserved right unsuppressed by water quality in establishing relevant WQS; and 3) establish water quality criteria to protect the Tribal reserved right where the state has adopted designated uses that either expressly incorporate protection of the Tribal reserved right or encompass the right. The latter requirement includes ”developing criteria to protect right holders using at least the same risk level… as the [s]tate would otherwise use to develop criteria to protect the [s]tate’s general population” (i.e., non-right holders). The rule also requires EPA to: 1) provide assistance with evaluating Tribal reserved rights upon request by states or right holders; 2) review WQS adopted by states and authorized Tribes to determine whether they appropriately considered applicable Tribal reserved rights; and 3) ”initiate the Tribal consultation process with the right holders” to inform this review. Several states, including Idaho, North Dakota, and Alaska, have challenged the final rule in a case still pending in the District of North Dakota.

B. CWA Sections 304 and 306 – Criteria, Guidelines, and Performance Standards

On January 23, 2024, EPA published a proposed rule “to revise the technology-based effluent limitations guidelines and standards (ELGs) for the meat and poultry products point source category.” The rule outlines several options for targeting the discharge of nutrients and other pollutants (e.g., nitrogen and phosphorus), including more stringent effluent limitations and pretreatment standards for indirect dischargers (i.e., facilities that introduce wastewater to Publicly Owned Treatment Works (as opposed to facilities that discharge directly into the waters of the United States)) and revised production thresholds. EPA’s preferred regulatory option would include “new phosphorus limits and revised nitrogen limits for large direct dischargers and new pretreatment standards on certain conventional pollutants for large indirect dischargers.” EPA issued this proposed rule pursuant to its ELG Program Plan 15, which governs, in part, EPA’s ELG program for addressing nutrient releases from meat processing point sources. Public comments on the rule were accepted through March 25, 2024, during which EPA received over 20,000, and the agency has not yet issued a final rule.

On May 9, 2024, EPA issued a final rule that updates requirements for wastewater discharge from steam electric power plants, with an emphasis on water discharged from coal-fired power plants. The final rule leaves in place previously-set requirements and adds new requirements that certain subcategories of electric generating units cease the combustion of coal by 2028 and by 2034, respectively. The rule also sets the following ELGs based on Best Available Technology Economically Achievable:

• A zero-discharge ELG for all pollutants in three categories of discharge (flue gas desulfurization wastewater, bottom ash transport water, and combustion residual leachate).
• A nonzero ELG for “mercury and arsenic in unmanaged [combustion residual leachate] and for legacy wastewater discharged from surface impoundments during the closure process if those surface impoundments have not commenced closure under the Coal Combustion Residuals regulations as of [July 8, 2024].”

EPA estimates that the rule will reduce pollutant discharges by 660 to 672 million pounds per year. The rule is being challenged in the Eighth Circuit, and in October, the court denied a stay of the rule without explanation. Thus, the rule has gone into effect while the appeal moves forward.

C. CWA Section 401 – Water Quality Certification

FERC seeks to amend its regulations in order to limit the time states and tribes have to evaluate an applicant’s request for water quality certification under Section 401 to one year. Section 401 provides that states must rule on certification requests within “a reasonable period of time (which shall not exceed one year).” State environmental authorities have sometimes asserted that a timeframe of one year is insufficient for them to gather information and evaluate applications, and therefore have sought to extend this period by requesting that an applicant withdraw and resubmit its request. FERC’s proposed rule would limit this practice by providing that the reasonable period of time during which the certifying authority may act on the water quality certification request is one year from the certifying authority’s receipt of the request. FERC proposed the rule on June 6, 2024, and comments were due on July 8 but FERC has not yet taken further action on the proposal.

D. CWA Section 402 – National Pollutant Discharge Elimination System (NPDES)

On April 16, 2024, EPA published its Clean Water Act Methods Update Rule for the Analysis of Effluent, finalizing changes to the test procedures that industries and municipalities must use to analyze wastewater and other samples when reporting under the NDPES permit program. Section 304(h) of the CWA requires EPA to “… promulgate guidelines establishing test procedures for the analysis of pollutants that shall include the factors which must be provided in any … permit application pursuant” to Section 402. EPA expects these revisions to help regulated entities meet monitoring requirements and improve data quality.

On May 9, 2024, EPA issued final Supplemental Effluent Limitations Guidelines and Standards for the Steam Electric Power Generating Point Source Category. The revised technology-based effluent limitations guidelines and standards apply to “flue gas desulfurization wastewater, bottom ash transport water and legacy wastewater at existing sources, and combustion residual leachate at new and existing sources.” The standards are estimated to reduce pollutant discharges from these sources by 660 to 672 million pounds per year.

On October 31, 2024, EPA issued a notice of two proposed actions regarding the Charles River, Mystic River, and Neponset River watersheds in Massachusetts. First, the notice proposes a “Preliminary Designation of certain stormwater discharges for commercial, industrial and institutional properties" in these watersheds for regulation under the NPDES permit program. Second, EPA released a Draft NPDES General Permit for these discharges. The Draft Permit regulates phosphorus as an indicator parameter for all regulated pollutants. All permittees would be required to develop, implement, and maintain a Stormwater Pollution Control Plan to reduce phosphorus from stormwater discharges by specific percentages. The public comment period for both actions ended on January 29, 2025.

E. CWA Section 404 – Wetlands, including Wetlands, including Waters of the United States (WOTUS)

On December 11, 2024, the EPA finalized an update to the CWA Section 404 Tribal and State Assumption Program regulations, the first revision since 1988. Section 404(g) authorizes states and Tribes to assume permitting responsibilities for discharges of dredged or fill material into certain waters, while the Army Corps of Engineers retains jurisdiction over waters like navigable rivers. Currently, only Michigan, New Jersey, and Florida have approved Section 404 programs, and no Tribes have assumed authority. The 2024 Rule addresses longstanding requests for clarity and transparency in the assumption process. It specifies what must be included in program descriptions and establishes criteria to ensure that state or Tribal programs are no less stringent than federal requirements. The rule clarifies jurisdiction over retained waters, distinguishing which permits applicants should seek from states, Tribes, or the Corps. It also includes streamlined procedures for program approval, allowing a transition period of up to 120 days after EPA approval for states and Tribes to take over administration. The rule provides new guidelines for compensatory mitigation, requiring federal review of some mitigation plans, and addresses long-term permitting for projects extending beyond the five-year limit set by the CWA. Additionally, the update includes clearer enforcement provisions, aligning compliance standards with those for other CWA programs. To enhance collaboration, the rule expands opportunities for Tribal input on permits issued by other jurisdictions and ensures that EPA oversight of assumed programs is more transparent.

III. Administrative

A. CWA Sections 304 and 306 – Criteria, Guidelines, and Performance Standards

In September 2024, pursuant to CWA section 304(a)’s mandate that EPA “develop and publish . . . criteria for water quality accurately reflecting the latest scientific knowledge,” the agency published three documents meant to assist states in developing their respective WQSs for the protection of aquatic life in relation to several polyfluoroalkyl substances (PFAS):

• Perfluorooctanoic Acid (PFOA);
• Perfluorooctane Sulfonate (PFOS); 
• Eight Data-Limited PFAS: PFBA, PFHxA, PFNA, PFDA, PFBS, PFHxS, 8:2 FTUCA, and 7:3 FTCA.

In the two recommended Ambient Water Quality Criteria (AWQC) documents for PFOA and PFOS, EPA “provides a critical review of all aquatic toxicity data identified in the EPA’s literature search for” the various substances, “quantifies the toxicity” of the substances, and “provides criteria to protect aquatic life in freshwater from the acute and chronic toxic effects” of the substances. As EPA notes in its notice of publication for these recommended AWQCs, the agency’s “recommended water quality criteria are not regulatory, nor do they automatically become part of a State’s water quality standards.” Instead, states “can establish water quality criteria based on the EPA’s recommended criteria, modify recommended criteria to reflect site-specific conditions, or develop proposed standards using other scientifically defensible methods.”

In the aquatic life benchmark document for the eight selected polyfluorinated substances, EPA similarly “provide[s] information that states and authorized Tribes may consider in their water quality protection programs.” However, EPA derived these informational values using the “limited high quality toxicity data available,” which do not meet EPA’s “minimum data requirements.”