States and EPA Work to Address the Challenges of NPDES Permitting for Indirect Discharges

January 20, 2026
Brenda H. Gotanda, Esq.
MGKF Special Alert - 2026 Federal Forecast

EPA and the States have been confronting the many challenges associated with implementation of the permitting required by the landmark decision of the U.S. Supreme Court in County of Maui, Hawaii v. Hawaii Wildlife Fund, 140 S.Ct. 1462 (2020). In Maui, the Court ruled that the federal Clean Water Act requires a National Pollutant Discharge Elimination System (NPDES) permit for the discharge from a point source of pollutants that reach navigable waters (also known as waters of the United States or WOTUS) after traveling through groundwater if that indirect discharge is the functional equivalent (FE) of a direct discharge from the point source into the WOTUS. The regulatory agencies have been working to develop strategies to address the difficulties in identifying, prioritizing, and permitting the multitude of indirect discharges that may now require NPDES permits. While it has been five years since the Maui ruling, there are still many issues to resolve given the complexity of subsurface discharges to groundwater, determining functional equivalence, and developing appropriate permit terms and conditions.

EPA has a webpage devoted to this issue with agency guidance and responses to over 25 Frequently Asked Questions (FAQs) regarding the permitting of discharges that travel through groundwater to surface waters. The FAQs address topics such as application of the factors that the Supreme Court identified as potentially relevant to determining whether a discharge is the FE of a direct discharge. Those FE factors include: (1) transit time, (2) distance traveled, (3) the nature of the material through which the pollutant travels, (4) the extent to which the pollutant is diluted or chemically changed as it travels, (5) the amount of pollutant entering the navigable waters relative to the amount of the pollutant that leaves the point source, (6) the manner by or area in which the pollutant enters the navigable waters, and (7) the degree to which the pollution (at that point) has maintained its specific identity. The Maui decision noted that these and other factors may be relevant to determining whether an indirect discharge is similar enough to a direct discharge to be functionally equivalent and to require a NPDES permit. It also postulated that future cases and agency guidance, rulemaking, and permitting would likely inform the issue going forward.

The EPA FAQs state that facility operators with releases to groundwater are, in the first instance, responsible for determining whether they need a NPDES permit for the discharge, and they should request a meeting with their permitting agency to help identify the information that the agency will need to review the FE analysis and process the application. They also state that while the FE analysis is necessarily site-specific, a general permit approach could be used by permitting agencies for certain types of discharges.

EPA’s webpage states that it was last updated in October 2025, which suggests that it reflects the current position of the Trump Administration. Notably, EPA’s guidance document posted on the website (“Applying the Supreme Court’s County of Maui v. Hawaii Wildlife Fund Decision in the Clean Water Act Section 402 National Pollutant Discharge Elimination System Permit Program to Discharges through Groundwater”) was initially published for comment by the Biden Administration EPA on November 27, 2023 after it rescinded a guidance document on this same topic issued by EPA during the first Trump Administration in 2021. The 2023 guidance is still designated as “draft guidance,” however, and it remains to be seen whether the current Trump Administration EPA will finalize, modify, or replace the 2023 draft guidance or any of the posted FAQs.

Most states have been delegated authority by EPA to implement the federal NPDES permitting program and, as such, they are on the front lines of this issue with primary responsibility for sorting out how to go about implementing the Maui decision and for permitting indirect discharges that meet the FE threshold.

A primary example is in Hawaii, where the Department of Health Clean Water Branch (DOH) has responsibility for implementing the federal NPDES program. Hawaii has many subsurface-type discharges (e.g., underground injection control (UIC), on-site disposal systems (OSDS) with ground discharge, etc.) that historically have not received NPDES permits and DOH has expressed concerns about the potential for this FE permitting effort to overwhelm its limited staff and resources. As such, it has been working to develop an implementation strategy and meeting with stakeholders to gather input. It held five stakeholder workshops in 2024. In those workshops, DOH identified the following as the overall goals for its strategy:

Identify potentially affected facilities

  • Depending on what types of facilities are included, universe could be over 100,000 potential permittees

Prioritize facilities for regulatory coverage

  • DOH is working to create “functional equivalency scores” as part of a ranking system to help prioritize permitting efforts

Develop a permitting strategy that:

  • Acknowledges both general permits (GPs) (for similar types of facilities) and individual permits may be needed.
  • Requires facilities to make the decision to seek permit coverage in accordance with the longstanding principles of the NPDES program.
  • Includes FE discharge determination criteria for applicability.
  • Creates regulatory certainty for potentially affected facilities.
  • Addresses the new FE requirement using DOH’s current limited resources.
  • Creates cross-programmatic consistency across affected DOH programs regarding UIC, wastewater reuse, NPDES permits, OSDS approvals, etc.
  • Promotes “no discharge” alternatives, such as wastewater reuse.

Determine what is needed to support the permitting strategy (e.g., revisions to statutes and rules, resources)


Some of the NPDES FE permitting challenges identified during the DOH stakeholder workshops included the following:

  • Determining functional equivalency and identifying applicable facilities.
  • Potential high number of applicable facilities and comparatively low permitting resources.
  • Appropriately identifying pollutants of concern while accounting for subsurface dilution and chemical changes due to transit time, distance traveled and contact with different substrates and pollutants contained in the groundwater.
  • Assessing the potential impacts on a surface water - does the discharge cause or contribute to an exceedance of applicable water quality?
  • Establishing permit limits without knowledge of dilution or potential chemical changes.
  • Low nutrient water quality criteria in Hawaii.
  • Identifying discharge location(s).
  • GPs are challenging to create with different facility types and pollutants.
  • TMDLs can be difficult to address in a GP.
  • Discharger education and understanding of the NPDES program.
  • Feasibility of new dischargers to comply.

As part of its implementation strategy, DOH is working to develop one or more NPDES general permits for similar types of FE discharges, which may help to ease the permitting burden on the agency and permittees.

Throughout the coming year, we expect to see more courts and agencies across the nation continue to confront the complex challenges of implementing the Maui decision with respect to indirect subsurface discharges. If you have questions about this article or NPDES permit requirements, please contact Brenda Gotanda.