Federal Baseline Water Quality Standards for Indian Reservations: Proposed Regulation Withdrawn

On May 5, 2023, the EPA Administrator published a proposed rule to promulgate federal baseline water quality standards (“WQS”) for waters on over 250 Indian reservations that do not have WQS in effect under the CWA. The rule, entitled “Federal Baseline Water Quality Standards for Indian Reservations,” was withdrawn in late 2024 before it could be finalized. However, it highlights why the CWA matters for Tribal Nations and the significance of the gap left in the current regulatory structure.

CWA protections have historically bypassed much of Indian Country. The CWA establishes federal minimum standards that both state and Tribal WQS must meet, but EPA-approved state WQS generally do not apply to Indian Country. However, this means that unless a Tribal Nation has adopted and obtained EPA approval for its own WQS, those Tribal waters do not benefit from CWA protections. Only 52 of the over 300 federally recognized Tribes with reservations have their own EPA-approved Tribal WQS. When the EPA administers Section 402 National Pollutant Discharge Elimination System (“NDPES”) permits for pollutants discharged into waters in most of the waterways that impact Indian Country, the conditions and requirements the EPA includes in the permit are not informed by Tribal priorities. This creates a gap where Tribal members and protected Tribal interests, such as fish and riparian ecosystems, are left vulnerable to greater contamination.

The failed rulemaking aimed to provide a stopgap framework for Tribal Nations by setting minimum standards for water quality protection in Indian Country. The existing process a Tribe must undergo to set its own WQS is time and resource intensive. First, a Tribal Nation must obtain TAS authorization from the EPA, and second, a Tribal Nation must promulgate and obtain EPA approval for those standards. The process to obtain TAS authorization was improved in 2016 to remove barriers to Tribal involvement, but it remains a significant regulatory burden. The baseline standards in the proposed rule would have safeguarded water quality until Tribes adopt their own WQS for these waters under the CWA. However, the EPA did not finalize the proposed regulation prior to the administration change in January 2025. Instead, the agency withdrew the proposed rule, leaving approximately 250 Tribal Nations without WQS for waters within their jurisdiction or the ability to influence the WQS that neighboring states may seek to implement. It is unlikely that the new administration will take up this rulemaking effort given the pushback from states and industry in other pro-Tribal CWA efforts.

Water Quality Standards Regulatory Revisions to Protect Tribal Reserved Rights, the “Tribal Reserved Rights Rule”: Litigation Paused and Petition Seeking Reconsideration Submitted

On April 26, 2024, the EPA Administrator signed a final rule to address how the EPA and states must consider Tribal reserved rights while establishing WQS. The “Water Quality Standards Regulatory Revisions to Protect Tribal Reserved Rights,” or the Tribal Reserved Rights rule (“TRR rule”), revised the WQS regulation at 40 C.F.R. § 131. Under the rule, when a state is undertaking its triennial WQS revision, if a Tribal Nation asserts off-reservation reserved rights in the WQS review process, the state must consider the use and value of the waters within its state jurisdiction for protecting and exercising Tribal off-reservation reserved rights, to the extent information and data are available. This is a procedural rule that is currently in effect but may soon disappear as a result of litigation or agency reconsideration under the current administration.

Tribal reserved rights are defined in this rule as rights to CWA-protected aquatic and/or aquatic-dependent resources reserved to Tribal Nations through treaties, statutes, or executive orders. There is no question many Tribal Nations have federal off-reservation usufructuary rights, such as rights to harvest, fish, or hunt in “usual and accustomed” places..[ii] However, while Tribal Nations can obtain TAS authorization to set WQS on their reservations, they cannot set standards off-reservation under the CWA, meaning Tribal Nations are not able to set the standards that protect their off-reservation rights. The only rights considered under the TRR rule are off-reservation rights that are expressly tied to aquatic and aquatic-dependent resources already protected under the scope of the CWA that require a certain level of water quality to be available for Tribal use.

The rule is composed of three main parts and can be found at 40 C.F.R. § 131.9. In short, it requires states to:

1. 1. consider the “use and value” of waters under their jurisdiction for protecting Tribal reserved rights;

1. 1. consider the anticipated future exercise of those reserved rights “unsuppressed” by inadequate water quality; and

1. 1. establish water quality criteria to protect Tribal reserved rights where they are expressly incorporated or encompassed by a state’s designated uses.

This rule outlines a framework for states to account for Tribal Nations’ usufructuary rights when setting state WQS. The components of the rule fit within the established purposes and goals to restore and enhance the quality of the United States’ waters and to protect the public health or welfare. The rule expressly recognizes the states’ traditional authority to set “designated uses” for a waterbody and does nothing to change that authority. However, it clarifies that states must implement a process to appropriately consider Tribal reserved rights whenever a Tribal Nation can provide information to support the existence of that right. States must consider those Tribal rights in the same manner as they are required to consider all “existing uses” of waters under their jurisdiction and must use that information to inform their decisions.

In creating this process, the TRR rule does not create new obligations. Instead, it serves to prevent states from overlooking or ignoring Tribal rights to use state-managed waters. Under the CWA, states are required to reassess their WQS every three years in a triennial review. States are also required, as part of their WQS, to adopt an antidegradation policy that protects the level of water quality supporting existing uses.[iii] These requirements do not come from the TRR rule; they are central features of the CWA’s regulatory scheme for water quality standards. Many states already have ways of obtaining and considering information on Tribal usufructuary rights when setting their WQS, but not every state does, and some states refuse to. The TRR rule clarifies and makes consistent the process that states must follow for fulfilling their CWA requirements.

Litigation History and Status:

In May 2024, a coalition of twelve states sued the EPA seeking to have the TRR rule overturned and vacated. The states brought their case in the U.S. District Court for the District of North Dakota and raised claims covering a wide variety of grounds. For example, they seek to have the rule declared unlawful because it is purportedly beyond the scope of EPA’s authority under the CWA. They also claim that the rule violates the Tenth Amendment’s anticommandeering doctrine – which prevents the federal government from requiring states or state officials to adopt or enforce federal law – by requiring the states to implement a federal policy.

Thirteen Tribal Nations, twelve of which are represented by Earthjustice, NARF, and Kanji & Katzen PLLC, intervened in the case to defend the rule. The Tribes refuted the states’ arguments and highlighted the harms caused by the ad-hoc and inconsistent way Tribal reserved rights have been considered by states prior to this rule. They also outlined states’ legal obligations to respect Tribal reserved rights, which are federal law.

On February 10, 2025, the judge in the case granted the EPA’s motion to stay the case due to the change in the administration. The litigation is currently paused while the EPA reconsiders its position and the rule itself.

Petition Seeking Reconsideration

On February 18, 2025, the Institute for Energy Research submitted a petition seeking reconsideration of EPA’s Tribal Reserved Rights Rule, 89 Fed. Reg. 35,717 (May 2, 2024), and rulemaking to amend 40 C.F.R. Part 131. The petition reiterates the states’ incorrect position that the TRR rule requires states to “interpret and enforce” Tribal rights. The petition, like the states, argues this is beyond the scope of the EPA’s authority under the CWA and contravenes the traditional authority vested in states to regulate land and water uses. The petition also argues  that accounting for Tribal reserved rights in water quality standards would cause states to incur immense costs, despite the reality that the CWA already requires many of the costs associated with the TRR rule. These include the costs of: reviewing the standards, which states must do every three years; considering existing uses of jurisdictional waters; and ensuring public participation.

Because the TRR rule is a final rule, any move to rescind or change the language of the rule will require the agency to conduct a rulemaking process, with a notice and comment period. The petition asks the EPA to initiate this process.

Next Steps:

It is likely that the EPA will begin the process of rescinding the rule. NARF will provide updates in The Headwaters Report if the agency proposes to rescind the rule and begins accepting comments.

Waters of the United States (WOTUS) Guidance and Rulemaking: EPA Published Notice of Rule Reconsideration; Currently Conducting Tribal Consultation.

“Water of the United States” (as noted above, known by its shorthand as WOTUS) is a threshold term in the CWA that establishes the geographic scope of federal jurisdiction under the CWA. The term “navigable waters,” defined in the CWA as “the waters of the United States, including the territorial seas,” underlies many CWA programs, including Section 303 (water quality standards and total maximum daily loads), Section 311 (oil spill programs, Section 401 (water quality certifications), Section 402 (pollutant discharge permits), and Section 404 (dredge and fill discharge permits). The definition of WOTUS defines the scope of CWA protections, which means its definition matters for Tribal Nations that use delegated authority under the CWA to manage and protect waters within their jurisdictions. However, there is no statutory definition for WOTUS, leaving that definition to agency regulation. The most recent Supreme Court decision addressing the definition of WOTUS is Sackett v. EPA, 598 U.S. 651 (2023).

Prior to the Sackett decision, WOTUS was defined by the “significant nexus” standard, i.e., a water or wetland needed to possess a “significant nexus” to waters that are, were, or could reasonably be made to be navigable, or to “significantly affect” such waters. In January 2023, the EPA and Army Corps promulgated a final rule, the Revised Definition of “Waters of the United States,” incorporating the “significant nexus” standard. However, in Sackett, the Supreme Court rejected the “significant nexus” standard and instead affirmed a different interpretation: that the CWA only protects “relatively permanent” waters, and that wetlands are only protected where they have “continuous surface connection” to, or abut, navigable waters in their own right. As a result of the Court’s ruling in Sackett, the agencies amended the 2023 rule to remove the “significant nexus” standard, thereby drastically limiting the CWA’s application to wetlands and leaving many ephemeral streams – particularly in the desert southwest – without protection. Nevertheless, the agencies continued to interpret the “continuous surface connection” requirement as being met if the wetlands in question were connected by a “discrete feature” to water falling under CWA jurisdiction. Discrete features include features like ditches that fall outside CWA jurisdiction on their own (i.e., non-jurisdictional ditches).

Now, the agencies are once again seeking to revise the rule on the basis that it does not adequately comply with the Sackett decision and needs to be further narrowed, including clarification that non-jurisdictional discrete features cannot establish continuous surface connection. The agencies are therefore particularly focused on: (i) the scope of “relatively permanent” and to what features that phrase applies; (ii) the scope of “continuous surface connection” and to which features that phrase applies; and (iii) the scope of what counts as a jurisdictional ditch. The forthcoming revisions to the WOTUS definition have significant implications for Tribal Nations seeking to use CWA regulatory programs to protect wetland and ephemeral water features within their jurisdictions from any potential negative impacts from federally permitted projects, because CWA protections, including applicable water quality standards and permitting requirements, will no longer apply to those waters.

Guidance on Proper Implementation of “Continuous Surface Connection” Under the Definition of “WOTUS” Under the CWA

On March 12, 2025, EPA and the Army Corps issued a joint memorandum defining “adjacent wetlands” as only those wetlands that “directly abut” jurisdictional waters (WOTUS, where CWA applies), thereby narrowing the interpretation of “continuous surface connection” as implemented by the administration after the Sackett decision. This is agency guidance, as opposed to a formal regulation, and does not have the force of law. Practically, however, it informs the public of how the EPA and the Army Corps intend to interpret WOTUS.

WOTUS Notice: The Final Response to SCOTUS; Establishment of a Public Docket; Request for Recommendations

On March 24, 2025, EPA and the Army Corps issued a notice in the Federal Register stating their intent to engage with stakeholders and gather recommendations on the meaning of key terms from Sackett to inform any potential future administrative actions to clarify the WOTUS definition.

Next Steps, Tribal Participation Opportunity:

The EPA and Army Corps have not yet proposed a revised regulatory definition of “WOTUS”. However, the agencies are accepting written recommendations from the public until April 23, 2025 (Docket No. EPA-OW-2025-0093). The agencies are looking for recommendations in three main areas: (i) the scope of “relatively permanent” and to what features that phrase applies; (ii) the scope of “continuous surface connection” and to which features that phrase applies; and (iii) the scope of jurisdictional ditches.

In addition, the agencies have initiated consultation with federally recognized Tribes. Information on these consultation efforts, including contact information, is available here. The anticipated timeline for the Tribal consultation and coordination period is expected to extend from March 21, 2025 until May 20, 2025. The agencies are holding two Tribal Listening Sessions in advance of publication of the proposed rule. The first was on March 31, 2025, and it included a presentation by the EPA on the need for a revised rule. The second will occur on April 30, 2025 at 1:00pm ET (registration information available here). Tribal Nations may also attend the public listening sessions, which are being scheduled. In addition, Tribal Nations are encouraged to request government-to-government consultation with the agencies to discuss concerns and recommendations. The agencies recommend that government-to-government consultation meetings be scheduled by May 20, 2025, by emailing CWAwotus@epa.gov. However, it is important to note that the federal government’s obligation to consult with Tribal Nations on a government-to-government basis in this rulemaking process does not end on May 20, 2025.

After the recommendation period is closed, the EPA and Army Corps will publish the agencies’ proposed language for the revised rule. NARF will update the Headwaters Report when the agencies propose revised language and begin accepting public comments.

Petition to Reconsider the CWA Section 401 Certification Improvement Rule: Petition Submitted; No Agency Action Yet

The Institute for Energy Research filed a petition requesting that the EPA reconsider and rescind the Section 401 Certification Improvement Rule finalized in 2023 and reinstate the 401 Certification Rule promulgated under the first Trump administration in 2020. This petition is particularly relevant for Tribes because, except for the legal interpretation put forth in the 2020 rule, Section 401 certification regulations have provided significant deference to Tribal sovereignty within the structure of the CWA. The regulations offer authorized Tribes the ability to condition or veto projects that violate the Tribe’s WQS and other water quality-related Tribal laws, including Tribal water codes. The 2020 rule had severely undermined the ability for states and authorized Tribes to review and certify, place conditions on, or veto, federally permitted projects that would degrade water quality within their jurisdiction.

For an overview of the importance of the Water Quality Certification Program under Section 401 to Tribes, read An Introduction to the Clean Water Act.

The petition advocates for a definition of the scope of certification that would once again effectively strip the authority of a Tribe to condition or veto an entire project and would limit the scope of Section 401 certification significantly. The petition argues the CWA must be interpreted more narrowly to limit the scope of certification. The 2023 Certification Improvement Rule currently defines the scope of certification as consideration of impacts (a) from the activity as a whole, encompassing point and non-point sources (b) on navigable waters and intrastate waters that (c) violate the CWA or any other appropriate requirement of State or Tribal law that has some relation to water quality. The petition seeks to narrow the scope of Section 401 certification authority to apply only to (a) discharges, not the project as a whole, that (b) impact the quality of “navigable” waters (i.e., waters covered by the “waters of the United States” (WOTUS) definition) and (c) violate EPA-approved state or Tribal water quality standards (WQS).

As discussed in the section on the WOTUS rulemaking process above[MK5] , any changes to the definition of WOTUS will impact the scope of Section 401 certification authority. Moreover, the narrow scope of certification reintroduced in this petition would erase the ability of Tribes to deny certification based on the Tribe’s sovereign laws and regulations. This is particularly relevant where a Tribe has TAS authorization to provide Section 401 Certification and to set water quality standards, but it does not yet have EPA-approved standards, as is the case with over 30 Tribes.

The legal status of the 2020 rule that the petition seeks to mirror is currently in limbo. In September 2020, Earthjustice filed a lawsuit challenging the 2020 Trump-era rule on behalf of the Suquamish Tribe, Pyramid Lake Paiute Tribe, Orutsararmiut Native Council, Columbia Riverkeeper, and Sierra Club. In 2021, the U.S. District Court for the Northern District of California vacated and remanded the rule because it found that the EPA, which had requested the remand for reconsideration, would not readopt the rule. Then, in February 2023 the Ninth Circuit reinstated the rule on the grounds that the District Court had overstepped its authority when it vacated the rule without determining whether it was unlawfully adopted. This reinstatement was temporary, because the Biden administration finalized its Certification Improvement Rule in November 2023. However, the courts never found the 2020 rule unlawful, and it is likely that the same language would form the basis of a reconsidered rule under the current administration.

Next Steps:

The EPA has not taken any action on this petition yet. NARF will update The Headwaters Report if the agency proposes to revise or rescind the rule and begins accepting public comments. If you are interested in staying informed of potential litigation challenging a change to Section 401 certification regulation, please email your contact information and Tribal affiliation to water@narf.org.