Home / Missions / Regulatory Program and Permits / Water Quality Certification

Overview of Section 401 of the Clean Water Act

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 and authorized tribes where the discharge would originate are generally responsible for issuing water quality certifications. In cases where a state or tribe does not have authority, EPA is responsible for issuing certification. 33 USC 1341. Some of the major federal licenses and permits subject to Section 401 include:

  • Clean Water Act Section 402 and 404 permits issued by EPA or the Corps,
  • Federal Energy Regulatory Commission (FERC) licenses for hydropower facilities and natural gas pipelines, and
  • Rivers and Harbors Act Section 9 and 10 permits.

The CWA provides that certifying authorities (states, authorized tribes, and EPA) must act on a Section 401 certification request "within a reasonable period of time (which shall not to exceed one year) after receipt" of such a request. A certifying authority may waive certification expressly, or by failing or refusing to act within the established reasonable period of time. In making decisions to grant, grant with conditions, or deny certification requests, certifying authorities consider whether the federally licensed or permitted activity will comply with applicable water quality requirements, which include water quality standards, effluent limitations, new source performance standards, toxic pollutants restrictions and other appropriate water quality requirements of state or tribal law.

Once the federal licensing or permitting agency receives both the application for the license or permit and a certification, it must immediately notify EPA under the neighboring jurisdiction process set forth in CWA section 401(a)(2). A federal agency may not issue a license or permit for an activity that may result in a discharge into waters of the United States prior to the completion of the CWA section 401(a)(2) process.

Section 401 Rule Making

On September 14, 2023, the U.S. Environmental Protection Agency (EPA or the Agency) announced the final 2023 Clean Water Act Section 401 Water Quality Certification Improvement Rule (2023 Rule). The final rule is grounded in the fundamental authority granted by Congress to states, territories, and Tribes to protect water resources that are essential to healthy people and thriving communities over the past 50 years. On September 27, 2023, the final 2023 Clean Water Act Section 401 Water Quality Certification Improvement Rule was published in the Federal Register. The final 2023 Rule went into effect on November 27, 2023. More information on the final 2023 Rule is available here. 

Section 401 of the Clean Water Act (CWA) provides states and authorized tribes with an important tool to help protect the water quality of federally regulated waters within their borders, in collaboration with federal agencies. EPA's regulations at 40 CFR 121 address Section 401 certification generally. EPA also has water quality certification regulations for federally-issued CWA Section 402 permits that are subject to the Section 401 certification requirements (40 CFR 124.53-124.55). Other federal agencies may also have CWA section 401 certification regulations for their licensing and permitting programs.

*The Corps is not responsible for the review or approval of any Section 401 certifications. Please review the map below for Information about Certifying Authorities (CA) within the Albuquerque District. Contact the corresponding CA with questions regarding Section 401 of the CWA specifically, obtaining  Water Quality Certification information.

Tribal boundaries are derived from the US Census Bureau's TIGER/Line American Indian/Alaska Native/Native Hawaiian Areas (AIANNH), 2022. This information is prepared strictly for illustrative and reference purposes only and should not be used, and is not intended for legal, survey, engineering or navigation purposes.

NWP Water Quality Certification information where the State is the Certifying Authority

  • On January 8, 2026, the U.S. Army Corps of Engineers (Corps) published a final action in the Federal Register (91 FR 768) announcing the reissuance of 57 existing nationwide permits (NWPs) and one new NWP, as well as the reissuance of NWP general conditions and definitions with some modifications. These 57 NWPs will go into effect on March 15, 2026, and will expire on March 15, 2031. One NWP was not reissued.
  • NMED certified the following Nationwide Permits (NWPs) without permit-specific conditions or permit-specific denials: 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 16, 17, 18, 19, 20, 22, 23, 25, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 49, 50, 51, 52, 53, 57, 58, 59, and NWP 60, provided that General Conditions 1–8 are followed. NMED has granted certification for NWPs 14, 21, and 44 subject to permit-specific conditions and compliance with General Conditions 1–8. NWPs 13, 27, and 43 are denied certification only in the specific circumstances outlined in the denial conditions. Outside of those circumstances, these NWPs are granted certification provided General Conditions 1–8 are met.

  • NMED, Clean Water Act Section 401 WQC for 57 NWPs.

For more information about NMED's Surface Water Quality Bureau please visit their website linked below.

On January 8, 2026, the U.S. Army Corps of Engineers (Corps) published a final action in the Federal Register (91 FR 768) announcing the reissuance of 56 existing nationwide permits (NWPs) and one new NWP, as well as the reissuance of NWP general conditions and definitions with some modifications. These 57 NWPs will go into effect on March 15, 2026, and will expire on March 15, 2031. One NWP was not reissued.

WQC of NWPs in Colorado is covered by a provision in the state’s Water Quality Control Act, which reads as follows: “General or nationwide permits under section 404 of the federal act shall be certified for use in Colorado without the imposition of any additional conditions.” C.R.S. § 25-8-302(1)(f).  A copy of CDPHE's decision letter can be accessed here.

Please visit CDPHE's Water Quality Control Division website by clicking the link below.

On January 8, 2026, the U.S. Army Corps of Engineers (Corps) published a final action in the Federal Register (91 FR 768) announcing the reissuance of 57 existing nationwide permits (NWPs) and one new NWP, as well as the reissuance of NWP general conditions and definitions with some modifications. These 57 NWPs will go into effect on March 15, 2026, and will expire on March 15, 2031. One NWP was not reissued.

TCEQ certifies that any discharge associated with the activities authorized by NWPs 1, 2, 4, 5, 8, 9, 10, 11, 20, 23, 24, 28, 34, 35, 48, and 55 will comply with water quality requirements as required by Section 401 of the Federal Clean Water Act and pursuant to Title 30, Texas Administrative Code (TAC), Chapter 279.
The TCEQ conditionally certifies that any discharge associated with the activities authorized by NWPs 3, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 25, 27, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51, 52, 53, 54, 57, 58, 59, and A will comply with water quality requirements as required by Section 401 of the Federal Clean Water Act and pursuant to Title 30, Texas Administrative Code, Chapter 279.

A copy of TCEQs decision letter and list of Conditions of Section 401 can be found here.

For more information regarding TCEQ and Water Quality please visit their Water Quality website linked below.

Texas Natural Resources Code, §91.101, and Texas Water Code, §26.131, grant the RRC jurisdiction for water quality certifications for federal permits covering activities associated with the exploration, development, and production, including pipeline transportation, of oil, gas or geothermal resources that may result in discharges to waters of the United States. No person may conduct any activity subject to RRC jurisdiction pursuant to a USACE permit if that activity may result in a discharge into to waters of the United States within the boundaries of the State of Texas, unless the RRC has first issued a certification or waiver of certification under 16 Texas Administrative Code §3.93 (Rule 93).

  • The RRC conditionally certifies that the activities authorized by NWPs 6, 7, 12, 14, 16, 18, 19, 25, 38, 43, 46 and 58 should not result in a violation of Texas Surface Water Quality Standards as required by Section 401 of the Federal Clean Water Act and pursuant to 16 TAC §3.93.
For more information regarding RRC and Water Quality please visit their water quality website linked below.

NWP Water Quality Certification information on tribal lands where EPA is the Certifying Authority

The appropriate EPA regional administrator retains the responsibility to make Water Quality Certification (WQC) decisions on tribal lands where the tribe does not have this authority from EPA. EPA Regions 9, 8, and 6 provided the following information regarding WQCs on tribal lands under each region’s responsibility for the current Nationwide Permits.

EPA-R9 has responsibility under Section 401 of the Clean Water Act (CWA) to evaluate and certify water quality protections for federal permits and licenses issued for work on tribal lands (40 C.F.R 123.12(a)). There Section 401 WQC applies to any potential point source discharges from potential projects authorized under the proposed reissuance of the following U.S. Army Corps of Engineers (Corps) Nation Wide Permits (NWPs) into waters of the U.S. that occur within tribal lands where tribes do not have treatment in a similar manner as a state and lands with exclusive federal jurisdiction in the Albuquerque Corps District. the following letters were provide to our office by EPA-R9 in response to the reissuance of the 2021 Nationwide permits. For general inquiries please contact the EPA-R9 office by email at R9cwa401@epa.gov.

 

The EPA is making the CWA Section 401 certification decision for the 2026 Nationwide Permit reissuance in Indian country in non-Tribal trust lands within the Southern Ute Indian Reservation and in any other Tribal trust lands outside of the Reservation in the state of Colorado.

The U.S. Environmental Protection Agency is the certifying authority. 33 U.S.C. 1341(a)(1). In this case, the Pueblos of Cochiti, Jemez, Santo Domingo, San Ildefonso, Zia, Zuni, The Mescalero Apache Tribe, and Jicarilla Apache Nation do not have the authority to provide CWA Section 401 certification for projects within their respective Tribal land. Therefore, the EPA is making the CWA Section 401 certification decision for the 2026 Nationwide Permit reissuance in Indian Country in New Mexico.

  • EPA is granting certification without conditions for NWPs 4, 5, 6, 7, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54 and A. For NWPs that EPA grants without conditions, EPA has determined that the activity will comply with the applicable water quality requirements, including any limitation, standard, or other requirement under sections 301, 302, 303, 306, and 307 of the CWA; any Federal and State or Tribal laws or regulations implementing those sections; and any other water quality-related requirement of State or Tribal law.
  • EPA is granting certification with conditions for NWPs 3, 12, 14, 57, and 58. For NWPs that EPA grants certification with conditions, EPA has determined that the activity will comply with the applicable water quality requirements, including any limitation, standard, or other requirement under sections 301, 302, 303, 306, and 307 of the CWA; any Federal and State or Tribal laws or regulations implementing those sections; and any other water quality-related requirement of State or Tribal law, subject to the conditions listed under the NWP below, pursuant to CWA Section 401(d).
  • Clean Water Act Section 401 Water Quality Certification for the 2026 U.S. Army Corps of Engineers Section 404 Nationwide Permits Reissuance, on behalf of Indian tribes that have not received Treatment in a Similar Manner as a State for Section 401 in EPA Region 6. 

NWP Water Quality Certification information on Tribal lands that are treated similarly to a state

Native American Tribes with water quality certifying authority from Environmental Protection Agency (EPA) have the responsibility to make WQC decisions on their lands. The following tribes located in the Albuquerque District have water quality certifying authority from EPA. Links to tribal WQC decisions received by the Albuquerque District are provided below. Contact information for each tribe can be found in the map above.

The Pueblo of Acoma has waived their water quality certification authority for all NWPs. The following letter was received by office in response to the 2026 reissuance of NWPs.

The Pueblo of Isleta denies water quality certification, without prejudice, for NWPs 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,25,27,29,30,31,32,33,34,36,37,38,39,40,41,42,43,44,45,46,48,49,50,51,52,53, 54, 57, 58, 59, and 60.

The link below contains the letter received from the Pueblo of Isleta in response to the 2026 Nationwide Permit reissuance.

 

The Pueblo of Laguna  received treatment in a similar manner as a state to administer water quality standards and certification programs  under the CWA Section 303(c) and 401, U.S.C. section 1313(c) and the 1341 by the EPA in December 2016. 

The Pueblo of Laguna certified all 2026 NWPs with one condition. A copy of their response including the referenced condition can be accessed in the link below.

 

 

Water Quality Certification for Pueblo of Nambe has been waived.

Water Quality Certification for the Picuris Pueblo has been waived.

Water Quality Certification for the Pueblo of Pojoaque has been waived.

All activities requiring authorization under Section 404 of the Clean Water Act within Pueblo of Sandia jurisdiction must obtain individual Section 401 water quality certification prior to permit authorization.

The Pueblo of Santa Ana grants water quality certification with conditions for all 2026 NWPs, see letter below for more details.

Water Quality Certification for Ohkay Owingeh has been waived.

The Santa Clara Pueblo provided a letter, linked below, conditionally certifying water quality standards for all Nation wide permits. This conditional certification is issued under the authority of the Santa Clara Pueblo Water Quality Code, adopted as amended by the Santa Clara Council Resolution No. 2003-27 (July 15, 2003). 

Water Quality Certification for the Taos Pueblo has been waived.

The Pueblo of Tesuque, by virtue of its treatment as a state status as conferred by the EPA, is authorized to certify Nationwide Permits (NWP) under Section 401 of the Clean Water Act. The pueblo has certified all NWPs with conditions.  Details of WQC can be found in the letter link below

 

The Navajo Nation  has denied Water Quality Certification (WQC) for all Nationwide Permits (NWPs). The detail of this decision can be found in the letter linked below.

The purpose of this letter is to notify the Corps that the Navajo Nation does not waive WQC, but respectfully denies certification for all NWPs and therefore will require that the Navajo Nation certify each individual permit. Accordingly, each individual applicant will need to apply for a Section 401 permit from the Navajo Nation EPA's Surface and Ground Water Protection Department's Water Quality Program (WQP). Anyone requesting to perform such activities must first obtain a project -specific  Section 401 WQC form the Navajo Nation EPA-WQP before proceeding under a NWP.

In 2018, the U.S. Environmental Protection Agency (EPA) approved the Southern Utes Indian Tribe’s application for treatment as a state to administer the Clean Water Act’s water quality standards and section 401 certification programs for water bodies on tribal trust land on the Southern Ute Indian Reservation (Reservation). Under Resolution No. 2015-15, adopted on February 17, 2015, the Southern Ute Indian Tribal Council delegated authority to the Division to exercise the Tribe’s Clean Water Act section 401 certification authority.

As stated in detail with in the letter linked below,  all projects that occur on tribal trust lands on the Southern Ute Indian Tribe Reservation, the Tribe certified 15 of the 57 NWPs with conditions. The Tribe  denied certification for 30 of the 57 NWPs, all “after-the-fact NWPs”, all provisional NWPs, and NWPs where the District or Division Engineer has granted a waiver on limits. The Division is waiving certification for 12 of the 57 NWPs. 

The Ute Mountain Ute Tribe has responsibility under section 401 of the Clean Water Act  to evaluate and certify water quality protection for federal permits or licenses issued for work on lands within the boundary of the Ute Mountain Ute  Reservation. The Tribe grants certification: NWP 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 27, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 48, 49, 50, 51, 52, 53, 54, 57, 58, 59. The Tribe Denies Certification for: NWPs: 1, 2, 8, 9, 10, 11, 24, 28, 35, and 60.

SPA Quick Links