Mind the gap: Where revised rulemaking fails to meet the science and legislative intent in defining waters of the United States

“Mind the gap” is a safety phrase first coined in 1968 on the London Underground to warn passengers about the space between the train and the platform edge. While engineering upgrades have reduced the physical gaps on the Underground, the phrase is now often used metaphorically to describe discrepancies in knowledge or, more recently, failures in lawmaking. In the case of headwaters, like streams and wetlands, and species reliant on those systems, the “gap” represents the lack of federal protection for a massive component of our freshwater ecosystems if the recently proposed Waters of the United States (WOTUS) rule is finalized as written. Unlike the London Underground, there is no simple engineering fix for the water quality and quantity impacts caused by dredging or filling streams and wetlands. Here, we explain how this gap results from failures across all three government branches. We then provide examples of what an improved WOTUS rule would encompass under agency authority and describe additional actions Congress can take after this rulemaking to better protect water quality and quantity for fisheries, including fish populations, their habitats, and the people who depend on them. With the passage of the Clean Water Act (CWA) in 1972, Congress aimed “to restore and maintain the chemical, physical, and biological integrity of the nation's waters.” To achieve this, the CWA aimed to eliminate pollutant discharges and restrict the dredging and filling of waters, including wetlands, to protect water quality for fish, wildlife, recreation, and human consumption. Congress wanted to make waters fishable and swimmable. Yet, Congress did not explicitly define WOTUS or specify exactly which waters required federal protection to achieve these goals, leaving the definition and extent of federal jurisdiction to rulemaking by the executive branch agencies (U.S. Environmental Protection Agency [EPA] and Army Corps of Engineers [USACE]). Because the legislative definition gap was left open, federal courts have played an outsized role in determining congressional intent. Cases such as SWANCC v. U.S. Army Corps of Engineers (2001) and Rapanos v. United States (2006) highlight the struggle to define the limits of federal agency jurisdiction under the CWA and the U.S. Constitution. Yet, despite decades of litigation, Congress has not updated the CWA to provide this needed clarity. The recent Sackett v. EPA (2023) Supreme Court of the United States (SCOTUS) decision resulted in a final interpretation that seriously curbs executive branch authority—wetlands must have a “continuous surface connection” with navigable waters to be protected. The SCOTUS majority decision in Sackett, and the justices’ questions during oral argument showed a lack of understanding regarding both the science of water connectivity and how legal experts from previous presidential administrations across the political spectrum interpreted the law (Sulliván et al., 2025). The court ignored the consensus of the scientific community (e.g., EPA, 2015) presented in the amicus brief filed by the American Fisheries Society and other scientific organizations, which detailed how intermittent hydrological connections contribute to biological or chemical connections (https://bit.ly/48NmpZW). The decision has crystallized into a rule that is substantially weaker than previous protections and is neither clear nor durable for determining jurisdiction (Figure 1). Variable definitions of Waters of the United States (WOTUS) under the Clean Water Act (CWA; modified from Sulliván et al., 2025). The proposed 2025 WOTUS definition narrows the scope of protection under the CWA compared to prior rules. The rule introduces the undefined “wet season” and stricter requirements for permanence and connection to a traditional navigable waterway (TNW). Water bodies facing weakened or eliminated federal protection include wetlands, ephemeral and intermittent streams, ditches, tributaries, and interstate waters. Illustration: Robert B. Keast. Public polls show that 72% of the U.S. public supports restoring federal protections of wetlands and streams to pre-rollback levels, and 94% of voters believe protecting the water in lakes, streams, and rivers is important (Walton Family Foundation, 2024). Yet, the proposed WOTUS rule further weakens these protections. Under the new rule, wetlands must have water throughout a yet-to-be-defined “wet season” and maintain a continuous surface connection with navigable water. Wetlands that dry during the wet season, or those separated by structures like levees, berms, or roads, will not be protected. Wetlands in a mosaic will be subject to individual agency delineation. Given the changes post-Sackett and from the proposed rulemaking, the most restrictive interpretation of the change projects up to 84% of wetlands that previously required a federal permit to dredge or fill would no longer be covered under the CWA (Natural Resources Defense Council, 2025). Streams must be relatively permanent to be covered under the rule, and this permanence will be judged based on flow during the wet season. Intermittent streams may be protected if they flow the entirety of the wet season. Jurisdiction for tributaries is nullified if flow passes through a non-jurisdictional water feature such as subterranean flow, culvert, or dam. Streams located upstream of a section that lacks flow during the entirety of the wet season will be outside jurisdiction. Bodies of water that are part of effluent systems for waste treatment may no longer have protection. This rule will also include a groundwater exemption. Even though groundwater is not regulated under the CWA, in County of Maui v. Hawaii Wildlife Fund, SCOTUS held that a point source discharge to WOTUS through groundwater requires a permit if the result is a functional equivalent of a direct discharge. If the final rule protects only perennial waters, federal jurisdiction could lose up to 8 million miles of streams (Natural Resources Defense Council, 2025). This legal definition conflicts with water connectivity science (EPA, 2015). Headwaters process and retain significant nutrients (e.g., nitrogen), protecting the chemical integrity of downstream navigable waters (Alexander et al., 2007). Headwater streams (first through third order) comprise roughly 53% of U.S. streams and 79% of total stream length (Colvin et al., 2019; Nadeau & Rains, 2007). Crucially, 60% of U.S. streams flow only seasonally or after precipitation, and these provide over half the volume of downstream waters (Brinkerhoff et al., 2024; EPA, 2015). These small streams, springs, and out-of-channel wetlands occur across a wide range of climatic, geologic, riparian, and biogeographic settings (Colvin et al., 2019; Meyer et al., 2007). They expose biota to diverse thermal, hydrologic, and chemical regimes (Meyer et al., 2007). Despite covering less than 1% of Earth’s surface, freshwater habitats house over half of all known fish species (Fricke et al., 2025). In the USA, at least 731 native freshwater species exist and 59% have habitat preferences for springs, creeks, or headwaters for all or part of their life cycle (Frimpong & Angermeier, 2009; Page et al., 2013), e.g., juvenile Coho Salmon Oncorhynchus kisutch rely on intermittent streams for overwintering, even growing larger in intermittent streams compared to Coho in perennial streams (Wigington et al., 2006); similarly, intermittent streams in the Colorado River basin that dry for most of the year support spawning Flannelmouth Sucker Catostomus latipinnis, Bluehead Sucker C. discobolus, and Roundtail Chub Gila robusta, showing that loss of intermittent streams would have negative impacts on fisheries (Hooley-Underwood et al., 2019). The seasonal gap. Tributaries vital to fish, such as intermittent streams that flow regularly but connect on the surface seasonally, may have protections eliminated unless they conform to a rigid, yet-to-be-defined “wet season.” While the agencies recognize the importance of seasonal flow, the lack of a definition in the proposed rule may jeopardize clarity and further place waters at risk. This overlooks the utility of tools, such as the 1987 USACE wetland delineation manual, which successfully used stable and long-lasting indicators to identify wetland soils, hydrography, and plants, and required only inexpensive equipment to perform. The data gap. Defining a wet season is particularly challenging for understudied systems lacking long-term hydrography data. Streams that connect only after precipitation or snowmelt are at risk of destruction, despite providing critical flows for fish migration and spawning. The wetland protection gap: Under the most restrictive interpretation, a vast majority of wetlands that were previously covered will no longer require a federal permit to dredge or fill them. For the 24 states relying solely on the CWA, this creates a total regulatory vacuum, leaving those waters with no state or federal oversight (Sulliván et al., 2025). There is no simple fix to this challenge of defining federal jurisdiction over WOTUS; it is a legal definition that will leave a gap between the law and the scientific understanding of how damage to headwaters pollutes downstream navigable waters. Federal rulemaking: The EPA and USACE must strive to include science-based recognition that pollution in headwaters inevitably connects to navigable waters, even if the current legal environment is restrictive. Congressional action: The SCOTUS stated in court opinions that Congress failed to define WOTUS. Congress can amend the CWA to explicitly include the waters this rule excludes. State action: If Congress fails to act, state legislatures can adopt statutes that require agency permits for discharging pollutants and dredging and filling wetlands and streams, and require buffer zones to capture and process nonpoint source pollutants. Even model policies from politically conservative organizations have suggested more extensive frameworks for wetland mapping and protection (e.g., American Legislative Exchange Council, https://bit.ly/3YdWrK6) than this WOTUS version. Local planning: Municipalities and townships can adopt setback requirements for development around wetlands and streams in zoning ordinances to provide a final layer of defense for water quality, flood protection, and biodiversity security. Since 1972, the scientific community has solidified understanding of the integrated nature of upstream, downstream, seasonal, and groundwater systems (EPA, 2015). Even before this rule, U.S. policy continued to lag behind science. The current regulatory approach exacerbates this gap by protecting only the larger parts of the whole (e.g., navigation channels). This rulemaking ultimately leaves critical systems supporting drinking water, floodwater storage, and biodiversity unprotected, systems vital for our nation’s security and economic prosperity. There is no simple administrative fix. Until policymakers and lawmakers acknowledge that legal definitions of WOTUS must align with the physical reality of water connectivity, the gap will remain. No new data were generated or analysed in support of this research. None declared.