Water Quality Certifications on Tribal Lands and Lands of Exclusive Federal Jurisdiction in EPA's Pacific Southwest (Region 9)

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About CWA Section 401 Certifications

Under Section 401 of the Clean Water Act (CWA), a federal agency may not issue a permit or license to conduct any activity that may result in any discharge into waters of the United States unless a Section 401 water quality certification is issued, or certification is waived. States, Territories, and authorized Tribes where the discharge would originate are generally responsible for issuing water quality certifications. The certifying authority can either grant, deny, or condition a certification, or determine that a certification isn’t needed (a waiver). Usually, states issue these certifications. However, because states lack jurisdiction on most Tribal lands, the CWA requires the federal government – in this case EPA – to fulfill this role. In some circumstances, Tribes may assume this responsibility from EPA. EPA is also responsible for water quality certification on lands of exclusive federal jurisdiction.

A list of all the federally-recognized Tribes can be found at: Federally-Recognized Tribes in EPA's Pacific Southwest (Region 9).

For general Information About Clean Water Act Section 401 refer to Section 401 of the Clean Water Act.

Implementation Procedures

The most common federal permits subject to Section 401 certifications are CWA Section 404 permits for placing dredged or fill material in jurisdictional waterways and wetlands, including seasonally dry permanent creek beds or wetlands that are common on Tribal lands in the West. These permits are often needed for building roads, utility lines and other structures, or even ecosystem restoration or flood control. The U.S. Army Corps of Engineers (USACE) issues Section 404 permits, and coordinates with EPA or the applicable state or tribal government for the Section 401 certification.

Certifications may also be needed for Federal Energy Regulatory Commission hydropower licenses, Rivers and Harbors Act Section 9 and 10 permits, and CWA Section 402 permits for stormwater and wastewater.

During the certification review, EPA will consider any EPA-approved water quality standards. If a Tribe does not have EPA-approved standards, other Tribal water quality standards or regulations will be considered. Where a waterbody flows into an adjacent state, the state standards for the receiving water body are also taken into consideration.

Federal licensing and permitting agencies are also required to notify EPA when they receive a water quality certification for that license or permit from the State, Tribe, or Territory in which that discharge occurs. EPA then has 30 days to review that notice to determine if the discharge “may affect…the quality of the waters of any other state” or Tribe with “treatment in a manner as a state” (TAS) status. This is referred to as a neighboring jurisdiction determination. If the discharge “may affect” a neighboring jurisdiction, EPA is required to notify the other state or Tribe, the federal licensing or permitting agency, and the project proponent.

The 2023 401 Certification Rule and additional materials can be found on the 2023 CWA Section 401 Water Quality Certification Improvement Rule page.

For projects on Tribal lands in the Pacific Southwest with a discharge requiring a federal license or permit, the project proponent will need to submit a CWA §401 certification request to EPA. Certification request and materials should be sent to: R9cwa401@epa.gov. For additional information and questions, you may also contact Russell Huddleston (huddleston.russell@epa.gov) or Sahrye Cohen (cohen.sahrye@epa.gov), Wetland Section Manager.

CWA §401 Water Quality Certifications

Region 9 Geographic Jurisdiction for CWA Section 401 Certifications

Related Content

EPA is the Clean Water Act (CWA) Section (§)401 water quality certifying authority for water quality certifications on Tribal Lands, where Tribes do not have Treatment-as-a-State (TAS) for CWA 401, and lands of exclusive federal jurisdiction of the Pacific Southwest. EPA’s R9 geographic jurisdiction for certification includes Tribal lands where a Tribe or State does not have authority in Arizona, California, and Nevada, the Confederated Tribes of the Goshute Reservation in Utah, and some Tribal lands of the Navajo Nation in Utah and New Mexico.

Requesting a 401 Pre-certification Meeting and Certification

For projects where EPA is the certifying authority, request a pre-certification meeting by email at R9cwa401@epa.gov. After the pre-certification meeting is completed or waived, certification requests and materials may be submitted by email to R9cwa401@epa.gov. For additional information and questions, you may contact Region 9 401 lead, Russell Huddleston (huddleston.russell@epa.gov), or Wetlands and Oceans Section Manager, Sahrye Cohen (cohen.sahrye@epa.gov).

Request for Certification Required Contents (40 C.F.R. Part 121, Section 121.5)

If the request for certification is for an individual Federal license or permit, it shall be in writing, signed, and dated and shall include the following:

  • A copy of the Federal license or permit application submitted to the Federal agency;
  • and any readily available water quality-related materials that informed the development of the application.
  • A description of the proposed activity, including the purpose of the proposed activity and the type(s) of discharge(s) that may result from the proposed activity;
  • The specific location of any discharge(s) that may result from the proposed activity;
  • A map or diagram of the proposed activity site, including the proposed activity boundaries in relation to local streets, roads, and highways;
  • A description of current activity site conditions, including but not limited to relevant site data, photographs that represent current site conditions, or other relevant documentation;
  • The date(s) on which the proposed activity is planned to begin and end and, if known, the approximate date(s) when any discharge(s) may commence;
  • (6) A list of all other Federal, interstate, Tribal, state, territorial, or local agency authorizations required for the proposed activity and the current status of each authorization; and
  • Documentation that a pre-filing meeting request was submitted to the certifying authority in accordance with applicable submission procedures, unless the pre-filing meeting request requirement was waived.

If the request for certification is for the issuance of a general Federal license or permit, it shall be in writing, signed, and dated and shall include the following:

  • A copy of the draft Federal license or permit;
  • and any readily available water quality-related materials that informed the development of the draft Federal license or permit.
  • A description of the proposed activity, including the purpose of the proposed activity and the type(s) of discharge(s) that may result from the proposed activity;
  • The specific location of any discharge(s) that may result from the proposed activity;
  • A map or diagram of the proposed activity site, including the proposed activity boundaries in relation to local streets, roads, and highways;
  • A description of current activity site conditions, including but not limited to relevant site data, photographs that represent current site conditions, or other relevant documentation;
  • The date(s) on which the proposed activity is planned to begin and end and, if known, the approximate date(s) when any discharge(s) may commence;
  • (6) A list of all other Federal, interstate, Tribal, state, territorial, or local agency authorizations required for the proposed activity and the current status of each authorization; and
  • Documentation that a pre-filing meeting request was submitted to the certifying authority in accordance with applicable submission procedures, unless the pre-filing meeting request requirement was waived.

401 Certifications for the USACE CWA 404 Nationwide Permits and Regional General Permits

USACE Nationwide Permits

The U.S. Army Corps of Engineers (USACE) can approve a project’s filling of waters with either “standard” or “general” Clean Water Act 404 permits. EPA Region 9 evaluates general permits for a programmatic conditional water quality certification. This avoids most case-by-case reviews, as most fill projects under general permit 401 certifications are covered simply by notifying EPA and following conditions in the certification. “Nationwide” permits (NWPs) are one type of general permit that streamline approval of low-impact fills. There are 57 activity-specific NWPs that are issued as a group every five years.

USACE Regional Permits

Projects that do not meet the conditions specific to the Regional General Permit or Nationwide Permit 401 certifications must contact EPA for a case-by-case individual project certification according to the above procedure.

CWA Section 401(a)(2) Neighboring Jurisdiction Determinations for all 401 Water Quality Certifications

Clean Water Act (CWA) section 401(a)(2) requires federal licensing and permitting agencies to provide EPA with written notification of receiving both the federal license or permit application and either a certification or waiver from the state or Tribe in which the discharge originates. 33 U.S.C. 1341(a)(2). EPA then has 30 days to review that notice to determine if the discharge “may affect…the quality of the waters of any other state” or Tribe with “treatment in a manner as a state” (TAS) status. This is referred to as a neighboring jurisdiction determination.

Federal licensing and permit agencies must notify EPA within 5 days of receiving a permit/license application and the related water quality certification using the online Federal Agency Notification form.

Public Notice

Public notices will appear here when available.

Additional Resources

Tribal Programs in the Pacific Southwest

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Last updated on July 22, 2026