WOTUS Snapshots: Sailing Shifting Seas

In life, only three things are certain: death, taxes and ever-changing administration of the federal Clean Water Act (CWA). In the following pages, we provide an overview of actions taken under President Trump’s second administration since our last WOTUS update and describe what project proponents might expect in the coming months and years. As is perennially true with WOTUS, we expect litigation to follow any final action taken by federal agencies.

Early 2025 Developments

Expediting Permitting for Energy Projects

Last year, Executive Orders issued by President Trump directed federal agencies to identify ways to expedite permitting for energy supply, including by using CWA emergency permitting provisions, identifying ways to eliminate delays associated with permit processing more generally and taking advantage of general permits like the nationwide permitting program (NWP) under the CWA and permits by rule.

Reconsidering the Definition of WOTUS

In March 2025, the U.S. Army Corps of Engineers (Corps) and Environmental Protection Agency (EPA) issued a guidance memorandum on how the agencies should implement the U.S. Supreme Court’s decision in Sackett v. EPA (in which the U.S. Supreme Court narrowed the scope of WOTUS jurisdiction as it relates to wetlands). The guidance memorandum set forth a two-part test for determining whether a wetland (or other feature) is a WOTUS:

1. Is the water body adjacent to the subject wetland a traditionally navigable water or a relatively permanent water connected to a traditionally navigable water?
2. If yes, does the wetland have a continuous surface connection to that water body (i.e., does the wetland directly abut the water where it is difficult to determine where the water ends and the wetland begins)?

Where drought, low tide, or other circumstances cause temporary interruptions to surface connections, the guidance instructs the agencies to use case-by-case judgment.

No End Result Requirements Allowed for NPDES Permits

On March 4, 2025, the U.S. Supreme Court issued its opinion in City and County of San  Francisco v. Environmental Protection Agency, dealing with limits on the EPA’s authority in administering the National Pollutant Discharge Elimination System (NPDES) under CWA Section 402. In this case, the Court held that “end-result” requirements routinely imposed by the EPA in connection with NPDES permits (e.g., requirements relating to attaining conditions in receiving waters rather than controlling constituents in effluent from the discharging facility) are not permissible under the CWA. This pivotal opinion has significant implications for how NPDES permits are administered across the country.

In the majority opinion, the Supreme Court held that the CWA does not authorize the EPA to include “end-result” provisions in NPDES permits. The majority opinion explained that the enforcement responsibility for determining and implementing steps to achieve water quality standards falls within the EPA’s mandate and cannot be shifted onto permittees through general outcome-based language.

In California, where the NPDES permitting program is delegated to the state’s water boards, the State Water Resources Control Board has promulgated guidance in the form of a memorandum from its Office of Chief Counsel that counterintuitively limits the application of the Supreme Court’s holding to NPDES permits for point-source discharge NPDES permits and precludes its application to stormwater NPDES permits, 401 certifications and water quality permits (called Waste Discharge Requirements) issued under California’s Porter Cologne Water Quality Control Act.

New WOTUS Definition Proposed

On November 17, 2025, EPA and the Corps published a proposed rule titled “Updated Definition of ‘Waters of the United States’” to revise the current regulatory definition of WOTUS (Proposed WOTUS Rule). EPA and the Corps have issued five separate definitions of WOTUS since 2015, as detailed in our previous article. The Proposed WOTUS Rule would add or change definitions of key terms, remove certain interstate waters from WOTUS, simplify or modify certain exclusions for waste treatment systems, cropland and ditches and expressly exclude groundwater from WOTUS.

Drawing from the Sackett decision, the Proposed WOTUS Rule provides definitions for two key terms which relate to whether certain bodies of waters would qualify as WOTUS:

• Continuous surface connection means “having surface water at least during the wet season and abutting (i.e., touching) a jurisdictional water.”
• Relatively permanent means “standing or continuously flowing bodies of surface water that are standing or continuously flowing year-round or at least during the wet ”

One can portend that aspects of these definitions, such as what constitutes “wet season” will be the subject of great interest, debate and litigation.

The current Unified Agenda anticipated the EPA and Corps would publish a final rule in January 2026. Until that actually occurs, a patchwork of regulatory regimes apply as a result of broad injunctions issued by federal courts with respect to prior versions of the definition. The WOTUS definition issued (and later amended) under the Biden administration is the operative definition in 24 states including California, Washington, Arizona, Colorado, Maryland and New York, while the regulatory regime that was in place prior to 2015 applies in the remaining 26 states, including Texas, Alaska and Virginia.

As a result of Trump v. CASA (2025), in which the U.S. Supreme Court ruled that universal injunctions exceed judicial authority unless necessary for complete relief, it is unlikely that a federal court would issue a far-reaching injunction against any forthcoming WOTUS definition; however, it is possible there could be an injunction reaching areas within the jurisdiction of one or more circuit courts or that a court could vacate the final rule — which would likely have nationwide effect.

Reissuance of Nationwide Permits

CWA section 404 (Section 404) requires that activities resulting in dredge or fill within WOTUS obtain authorization from the Corps, even as the definition of WOTUS keeps changing. Many projects comply with Section 404 through the Corps’ NWP program.

On January 8, 2026, the Corps finalized 57 NWPs under CWA section 404, replacing 56 NWPs that were set to expire in March 2026 and issuing one new NWP (activities to improve passage of fish and other aquatic organisms), and also reissued NWP general conditions and definitions with some modifications. The NWPs went into effect on March 15, 2026, and will expire on March 15, 2031. The Corps regional divisions will finalize any regional conditions for the NWPs, and will determine which conditions for water quality certifications issued by States, Tribes and EPA will be incorporated as NWP conditions for those regions. On March 16, 2026, the Corps published a notice seeking public comment for potential future modifications to the NWPs to improve efficiency. That comment period closes on May 15, 2026.

As discussed below, NWP general conditions require that a proposed activity obtain a CWA section 401 (Section 401) certification from a state, tribe, or EPA affirming that the proposed activity will not violate water quality standards. In California, the State Water Board issues general 401 certifications for some of NWPs. Most recently, the State Water Board granted general 401 certification to 19 of the 2026 NWPs, which took effect on March 15, 2026 and are subject to certain terms and conditions.

The 19 California-certified NWPs are as follows: NWPs 1 (Aids to Navigation), 3(a) (Maintenance), 4 (Fish & Wildlife), 5 (Scientific Measurement), 6 (Surveys), 9 (Anchorage Area Structures), 10 (Mooring Buoys), 11 (Temporary Recreational Structures, 12 (Oil or Natural Gas Pipeline Activities), 13 (Bank Stabilization), 14 (Linear Transportation Projects), 20 (Oil or Hazardous Substance Response), 22 (Vessel Removal), 28 (Marine Modification), 32 (Completed Enforcement Actions), 36 (Boat Ramps), 54 (Living Shorelines), 57 (Electric Utility and Telecommunications) and 58 (Utility Line Activities for Water and Other Activities).

401 Certification Proposed Rule

Section 401 requires that any project seeking federal permits or licenses that could result in discharge of pollutants into WOTUS must obtain a water quality certification from the state or tribe in which the discharge originates. The water quality certification affirms that the proposed discharge will comply with the standards established in other parts of the CWA (e.g., effluent limitations, standards of performance, water quality standards and implementation plans).

How states, tribes and other jurisdictional authorities have implemented Section 401 certification has been subject to litigation and scrutiny over the years, and the EPA has reviewed and revised its Section 401 implementing regulations multiple times over several administrations. Most recently, in 2023, EPA issued revised Section 401 implementing regulations, which are still the subject of litigation. Issues in the litigation serve as topics for the new proposed rulemaking, including the latitude states have to impose certification conditions related to environmental concerns that are only indirectly related to water quality, as well as the flexibility certifying agencies have to take longer than one-year to act on a certification request.

On January 15, 2026, EPA published a proposed rule titled “Updating the Water Quality Certification Regulations” to implement changes to the Section 401 certification process (Proposed Section 401 Regulations) which would, among other things:

• Narrow the scope of states’ certification authority to prohibit imposition of conditions unrelated to water quality-related conditions on regulated discharges;
• Adopt a mandatory one-year deadline for certifying authorities to act on a certification request; and
• Prohibit imposition of conditions relating to general environmental protection.

If the rule is finalized as proposed, states and tribes would be constrained in what requirements they could impose through the Section 401 certification process, and in taking longer than one year to issue certifications.

Pursuant to the September 2025 Unified Agenda, the regulated community was anticipating that the rule would be finalized by January 2026 but there appears to be some delay, perhaps in part due to concerns about its defensibility. On April 8, 2026, eleven U.S. senators including California’s Alex Padilla sent a letter to EPA opposing the proposed rule.

Vacatur of Florida’s Delegated 404 Program

Section 404(g) authorizes states and tribes to administer the Section 404 permitting program within their jurisdictions where those states have been approved by EPA to do so. While 47 states and at least 84 tribes administer NPDES permitting under Section 402, only three states have been delegated authority under Section 404 (Florida, Michigan and New Jersey). In April 2026, the U.S. Court of Appeals for the D.C. Circuit (D.C. Circuit) affirmed a decision by the district court to vacate EPA’s approval of Florida’s application to administer Section 404 within that state on the basis that EPA’s approval violated section 7 of the federal Endangered Species Act (ESA).

ESA section 7 (Section 7) requires federal agencies to ensure that actions they authorize, fund, or carry out do not jeopardize ESA-listed species or result in destruction or adverse modification to designated critical habitat (Ad Mod). This determination is made in consultation with the U.S. Fish and Wildlife Service (USFWS) and/or National Marine Fisheries Service (NMFS) (collectively, the Service). Where an activity will adversely affect a listed species or critical habitat, but will not result in jeopardy or Ad Mod, the Service will issue a biological opinion (BiOp) describing, among other things, measures the agency must implement to reduce adverse effects. Where “take” of listed species will occur in connection with the activity subject to consultation, the Service will issue an incidental take statement (ITS), which authorizes take that occurs in connection with the activity under consultation.

Prior to EPA’s approval of Florida’s application for Section 404 delegation, EPA and USFWS engaged in Section 7 consultation, which resulted in USFWS issuance of a BiOp and ITS. The ITS authorized “take” associated with activities conducted by permittees under the delegated 404 program, and relied on a “technical assistance” program. Through that program, applicants for Florida’s delegated Section 404 permitting program would provide information concerning their activities’ effects on listed species and critical habitat and the State of Florida would review the information and determine whether additional measures should be implemented to avoid adverse effects. USFWS had the option (but not the requirement) to weigh in.

In 2024, the U.S. District Court for the District of Columbia held that the technical assistance process established by the BiOp was not a lawful substitute for the procedures and remedies enumerated in the ESA. On March 27, 2026, the D.C. Circuit upheld that decision in Center for Biological Diversity v. Zeldin (2026).

States including California, Arizona and Alaska have explored the option of assuming Section 404 program delegation in the past, but have never formally submitted an application to the EPA. If they or any other state choose to seek Section 404 delegation in the future, the holdings in Center for Biological Diversity v. Zeldin may result in greater project-level scrutiny under the ESA.

Looking Ahead: Federal Legislation, ESA Compliance and Litigation

Federal Legislation

While Congress recently has focused on streamlining federal environmental permitting and reducing unnecessary delay and red tape, no major federal legislation affecting CWA administration is currently pending. However, one pending House bill (H.R. 5566), introduced in September 2025 by Rep. Carbajal (D-CA), would extend sunset dates for three programs related to funding for drinking water infrastructure and publicly owned treatment works from 2026 to 2031. The bill would affect CWA sections 223(g) (1), 1459A(1) and 1459F(f)(1), and was referred to two committees and one subcommittee but has not moved since December 2025.

ESA

Projects needing “take” authorization have often used the consultation process established by Section 7 (see above for additional details concerning ESA consultation generally). This is because Section 7 contains statutory deadlines for agencies to make decisions (e.g., 135 days), while the ESA Section 10 permitting process for projects with no federal nexus contains no statutory deadlines and frequently takes more than two years (and sometimes upward of a decade). Project proponents frequently have used the Section 404 permitting process – including specifically the NWP process – as a trigger for obtaining “take” authorization through Section 7, as Section 7 applies only where there is a federal nexus.

One of the implications of the Supreme Court’s decision in Sackett is potentially limiting the opportunity for project proponents to utilize Section 7 for ESA “take” authorization in an expedited manner (and related limitation for project opponents to challenge final agency actions — i.e., verification of a project’s use of a NWP or USFWS’s issuance of a BiOp and/or ITS). Should the Corps and EPA adopt and implement a final definition of WOTUS in a form substantially similar to the Proposed WOTUS Rule, this circumstance would become even more common. Project proponents — particularly those located in the arid west — should ensure project planning includes a strategy for ESA compliance, where necessary.

Litigation

When and if finalized, there is a virtual certainty that any WOTUS definition and revised 401 certification rules will be challenged in multiple federal courts, which will create continued uncertainty for project planning and implementation. Project proponents should work closely with their qualified consultants and attorneys on permitting strategies, with particular consideration of each project’s unique attributes.

The content of this article is intended to provide a general guide to the subject matter. Specialist advice should be sought about your specific circumstances.