Unsettled Waters: Navigable Waters Protection Rule Narrows the Definition of “Waters of the United States”

Unsettled Waters: Navigable Waters Protection Rule Narrows the Definition of “Waters of the United States”

Client Alert


On January 23, 2020, the Trump Administration issued a final rule revising the definition of “waters of the United States” (WOTUS) under the federal Clean Water Act (CWA). The Navigable Waters Protection Rule narrows the definition of WOTUS—thereby narrowing CWA jurisdiction—and will surely face legal opposition.

Key Takeaways

  • The Navigable Waters Protection Rule, issued jointly by the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (the Corps), significantly modifies the scope of water bodies subject to regulation under the CWA, meaning that CWA permits will no longer be required for many water bodies that previously were regulated (or “jurisdictional”) water bodies. Notably, the rule excludes ephemeral water bodies and wetlands that are not “adjacent” to other jurisdictional waters.
  • The rule represents the culmination of a rulemaking process designed to scale back the scope of CWA jurisdiction, including repeal of the 2015 Clean Water Rule (the Obama Administration’s rulemaking that attempted to clarify the definition of WOTUS).
  • The Navigable Waters Protection Rule will go into effect 60 days after publication in the Federal Register. However, opponents of the new rule may seek a judicial stay of its effects. Because the Navigable Waters Protection Rule was preceded by a regulatory repeal of the 2015 Clean Water Rule, a judicial stay of the new rule’s implementation would reinstate the pre-2015 WOTUS regulatory scheme, returning the country to standards put in place in 1986. 
  • The new rule is likely to be dismantled if there is a change in administration following the 2020 presidential election.
  • Industries such as agriculture, construction, mining, and oil and gas, whose operations involve discharges (including by dredging or filling) to areas considered WOTUS will be affected by the new rule. Companies within these industries should carefully evaluate whether to seek CWA permits for planned activities not considered to impact WOTUS under the new rule, as legal challenges could impact its implementation, leaving some degree of regulatory uncertainty as the rule is tested.


The CWA regulates discharges to “navigable waters,” which the statute defines as “waters of the United States, including the territorial seas.” 33 U.S.C. § 1362(7). The scope of the terms “navigable waters” and “waters of the United States” is relevant under several CWA programs, including those statutory schemes governing discharges of dredged or fill material under Section 404, administered jointly by the Corps and EPA; discharges of pollutants from “point sources” under Section 402, delegated to most states for permitting under the National Pollution Discharge Elimination System; and spills of oil and hazardous substances under Section 311.

The Navigable Waters Protection Rule is the latest twist in a decades-long endeavor to define “waters of the United States” under the CWA. In 1985, the US Supreme Court held that the term “navigable waters” includes more than only those waters that would be deemed “navigable” in the “classical” or traditional sense. United States v. Riverside Bayview Homes, Inc., 474 U.S. 121, 133 (1985).

But the scope of the terms “navigable waters” and “waters of the United States” has remained difficult to define. The issue was revisited by the Supreme Court in Rapanos v. United States, 547 U.S. 715 (2006), where a divided Court offered two possible definitions, though neither commanded a majority of the Justices. Under one definition, offered by Justice Scalia and endorsed by three other Justices, “waters of the United States” are “relatively permanent” waters that hold a “continuous surface connection” to a traditionally navigable water. Under the second definition, proposed by Justice Kennedy in a concurring opinion, “waters of the United States” must have a “significant nexus” to a traditionally navigable water.

This splintered decision left the regulated community in a state of uncertainty because none of the five separate opinions commanded a majority of the Court, and because the proposed definitions did not align with well-understood principles of hydrology. In an effort to clarify the definitions, the Obama Administration published the Clean Water Rule in June 2015. The central feature of the 2015 Clean Water Rule is the significant nexus standard: The Obama rule would determine CWA jurisdiction on a case-by-case basis focusing on whether a particular area had a “significant nexus” to traditional navigable waters, interstate waters or wetlands, or the territorial seas. This approach meant that even isolated water bodies could be subject to CWA jurisdiction if there was an otherwise “significant nexus” to a navigable water. Litigation followed immediately, and the Sixth Circuit stayed the rule nationwide in October 2015. In re EPA, 803 F.3d 804 (6th Cir. 2015). That stay was lifted after the US Supreme Court held that the challenges to the rule needed to go to federal district courts, not directly to federal appeals courts. Nat’l Ass’n of Mfrs. v. DOD, 138 S. Ct. 617 (2018). Litigation challenging the 2015 Clean Water Rule is still ongoing.

On February 28, 2017, President Trump signed an Executive Order to kick off a plan to repeal the 2015 Clean Water Rule and replace it with a new rule.1 The Executive Order instructed EPA and the Corps to “consider interpreting the term ‘navigable waters,’ . . . in a manner consistent with the opinion of Justice Antonin Scalia in Rapanos v. United States, 547 U.S. 715 (2006).”

On December 11, 2018, EPA and the Corps issued a proposed rule to define “waters of the United States” in accordance with the Executive Order. Although the agencies received over 600,000 public comments on the proposed rule, the final Navigable Waters Protection Rule largely mirrors the 2018 proposed rule.

On October 22, 2019, EPA and the Corps published a separate final rule repealing the 2015 Clean Water Rule, and that repeal became effective on December 23, 2019.2 The agencies announced that, until publication of a new rule, they would implement the “pre-2015 [1986] Rule regulations . . . consistent with Supreme Court decisions and longstanding agency practice.” In December 2019, a coalition of 14 states and others sued EPA over its rollback of the Obama-era rule. New York et al. v. Wheeler, S.D.N.Y., No. 1:19-cv-11673 (filed Dec. 20, 2019). The suit alleges that the repeal of the 2015 Clean Water Rule—and reinstatement of the 1986 rule in the interim—is inconsistent with US Supreme Court case law. Plaintiffs also allege that EPA and the Corps made clear in the response to comments and summary for the Proposed Navigable Waters Protection Rule that a return to the 1986 rule is not workable: “[F]ollowing the Supreme Court’s opinions on the definition of ‘waters of the United States,’ particularly SWANCC and Rapanos, the 1986 Rule cannot be implemented as promulgated.” Revised Definition of “Waters of the United States” (Proposed Rule), 84 Fed. Reg. 4154, 4198 (Feb. 14, 2019) (citations omitted). Further, the lawsuit notes that the guidance documents on which the agencies relied in their repeal of the 2015 Clean Water Rule should have been subject to notice and comment rulemaking under the Administrative Procedure Act. New York and California are leading the charge in this suit.

Final Rule

The Navigable Waters Protection Rule defines jurisdictional waters and non-jurisdictional waters.

Jurisdictional waters include four categories of water bodies:

  1. The territorial seas and “traditional” navigable waters (like the Mississippi River);
  2. Perennial and intermittent tributaries to those waters;
  3. Lakes, ponds and impoundments that contribute surface flow to traditional navigable waters; and
  4. Wetlands adjacent to jurisdictional waters.

The final rule identifies 12 categories of waters that are non-jurisdictional waters, including groundwater, groundwater recharge structures, prior converted cropland, artificial lakes and ponds, stormwater runoff and stormwater control features, waste treatment systems, and “ephemeral features, including ephemeral streams, swales, gullies, rills, and pools.” “Ephemeral” is defined as “surface water flowing or pooling only in direct response to precipitation (e.g., rain or snow fall).”

The Navigable Waters Protection Rule rejects the Obama Administration’s Clean Water Rule’s case-by-case jurisdictional analysis. Instead, the new regulatory framework relies on the concept of a “typical year,” and defines as jurisdictional those waters that have a surface connection to a navigable water during such a typical year. According to agency guidance, a “typical year” is “a calculation of normal precipitation, drought and other climatic conditions over a rolling 30-year period at a location of interest.”3

Anticipated Legal Challenges May Add Further Confusion

Many groups are already gearing up for litigation over the Navigable Waters Protection Rule; it is anticipated that states, environmental organizations and other interested parties will file suit as soon as the rule is published in the Federal Register. Lawsuits will undoubtedly seek to enjoin the rule, as occurred with the 2015 Clean Water Rule.

If the new rule ultimately is reviewed by the current Supreme Court, it may receive favorable treatment. In recent decisions, the Court seemed ready to narrow the definition of “waters of the United States,” noting that a broad definition allows regulators to assert jurisdiction over “270-to-300 million acres of swampy lands in the United States—including half of Alaska and an area the size of California in the lower 48 States.” United States Army Corps of Eng’rs v. Hawkes Co., 136 S. Ct. 1807 (2016) (quoting Rapanos).

If there is a change in administration following the November 2020 presidential election, however, the new administration would likely repeal the Navigable Waters Protection Rule and replace it with a more jurisdictionally expansive rule, again redefining WOTUS and potentially again unsettling regulatory certainty.

Many Affected Industries

Industries whose operations involve discharges to WOTUS, including agriculture, construction, mining, and oil and gas, will be affected by the new rule. As the new rule has not yet been interpreted by the courts, ongoing legal challenges, including the possibility of a stay, could result in forestalled implementation of the rule. Accordingly, companies should be prepared for the possibility of needing CWA permits for discharges to waters that would be non-jurisdictional under the new rule.


As was the case for the 2015 Clean Water Rule, the Navigable Waters Protection Rule has been the subject of vigorous debate, and the final rule is likely to face significant legal challenges. Regardless of how the new rule might be intended to affect CWA jurisdiction, it may have the opposite effect in practice. Instead of providing predictability and certainty for stakeholders and regulated entities, it is likely to prompt legal battles that will further perpetuate uncertainty about the scope of the CWA.

In the interim, companies and industries affected by the Navigable Waters Protection Rule should carefully monitor the legal status of the rule to evaluate projects and permitting strategies that take into account the unsettled waters ahead.



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