Water Quality Certification

Under Section 401 of the Clean Water Act (CWA), the US Army Corps of Engineers (Corps) cannot issue a permit to conduct any activity that may result in a discharge into waters of the United States unless a Section 401 water quality certification (WQC) is granted, verifying compliance with water quality requirements, or WQC is waived.  States and authorized tribes, where the discharge would originate, are generally the certifying authority (CA) responsible for  making WQC decisions.  In cases where a state or tribe does not have authority, the U.S. Environmental Protection Agency (EPA) is the CA responsible for making WQC decisions.  (see 33 CFR 325.2 [Individual Permits] and 33 CFR 330.4(c) [Nationwide Permits]).

On September 11, 2020, the EPA promulgated the new CWA Section 401 Certification Rule (85 Federal Register 42210) codified within the Code of Federal Regulations at Title 40, Part 121.  This rule sets forth a new process for requesting individual WQC , which includes new procedural requirements..  Additional information regarding the new rule can be found within the EPA Section 401 website at https://www.epa.gov/CWA-401 and within the USACE Albuquerque District-Regulatory Division special public notice, found at https://www.spa.usace.army.mil/Missions/Regulatory-Program-and-Permits/Water-Quality-Certification/.

  1. Important Considerations for Project Proponents:
    1. Before submitting a request for an individual Section 401 WQC to the CA (state/Tribe/EPA) , a project proponent must request a pre-filing meeting with the certifying authority at least 30 days prior to submitting the WQC request.  The certifying authority will determine whether the meeting will be held, but submittal of the request for a pre-filing meeting is required.
    2.  After the pre-filing meeting request has been submitted and 30 calendar days have elapsed, applicants may submit their requests for WQC which must be submitted to the CA and the Corps Albuquerque District-Regulatory Division (RD) concurrently
    3. The Rule outlines the nine (9) items required in the request, which are found at 40 CFR 121.5 (b).

  2. WQC Request Timeframes:

The Rule requires that action on a WQC request must be taken by the certifying authority within a reasonable period of time [40 CFR 121.6] determined by the federal licensing or permitting agency, but in no case later than one year after receipt of a certification request.  The RD will establish the reasonable period of time on either a categorical or case-by-case basis, according to criteria prescribed by the Rule. 

Within 15 days of receipt of a request for WQC, the RD will notify the certifying authority of the reasonable period of time to act on the certification request and the date upon which waiver will occur if the certifying authority fails or refuses to act on the certification request.  Once the certifying authority has received RD’s notice of the reasonable period of time, the certifying authority or project proponent may make a written request for extension, if necessary.  However, the reasonable period of time may not exceed one year.

  1. Post-certification Process – Determination of effect on neighboring jurisdictions:

In accordance with 40 CFR 121.12  of the Rule, the Corps shall notify the EPA within 5 days of receipt of a permit application and issued WQC. Within 30 days after receiving this notification, the EPA at his or her discretion may determine that the discharge from the certified project may affect water quality in a neighboring jurisdiction.  If the EPA determines that the discharge from the certified project may affect water quality in a neighboring jurisdiction, the EPA will notify the neighboring jurisdiction, the certifying authority, the Corps, and the project proponent within that 30 days. This neighboring jurisdiction will have 60 days to notify the EPA and Corps whether it has determined that the discharge will violate any of its water quality requirements, to object to the issuance of the permit, or to request a public hearing.

WQC for the 2021 Nationwide Permits (NWPs)

On January 13, 2021, the Corps published a final rule in the Federal Register (86 FR 2744) announcing the reissuance of 12 existing NWPs and four (4) new NWPs, as well as the reissuance of NWP general conditions and definitions with some modifications. These 16 NWPs went into effect on March 15, 2021 and will expire on March 14, 2026:

NWP 12 – Oil or Natural Gas Pipeline Activities
NWP 21 – Surface Coal Mining Activities
NWP 29 – Residential Developments
NWP 39 – Commercial and Institutional Developments
NWP 40 – Agricultural Activities
NWP 42 – Recreational Facilities
NWP 43 – Stormwater Management Facilities
NWP 44 – Mining Activities
NWP 48 – Commercial Shellfish Mariculture Activities
NWP 50 – Underground Coal Mining Activities
NWP 51 – Land-Based Renewable Energy Generation Facilities
NWP 52 – Water-Based Renewable Energy Generation Pilot Projects
NWP 55 – Seaweed Mariculture Activities
NWP 56 – Finfish Mariculture Activities
NWP 57 – Electric Utility Line and Telecommunications Activities

NWP 58 – Utility Line Activities for Water and Other Substances

In accordance with the U.S. Environmental Protection Agency’s (EPA’s) current water quality certification (WQC) regulations at 40 Code of Federal Regulations (CFR) Part 121, the Albuquerque District has reviewed Clean Water Act Section (CWA) 401 WQC decisions received from certifying authorities.  The Albuquerque District has determined that all accepted granted and denied WQC decisions in New Mexico satisfied the requirements set forth in 40 CFR 121.7. 

It is important to note that WQC was not granted for all 16 NWPs and that individual WQC will be required in some cases (see below for more information).  The following links access the WQC decisions applicable to the 16 NWPs above and explain when individual WQC is required:


New Mexico


Navajo Nation

WQC for the 2017 NWPs

There are 40 existing NWPs that were not reissued or modified by the January 13, 2021 final rule.  Those 40 NWPs were published in the January 6, 2017, issue of the Federal Register (82 FR 1860) and those NWPs remain in effect until they are modified, revoked or expire on March 18, 2022.  The WQC decisions associated with these NWPs remain in effect until these specific NWPs are modified, revoked or expired.  The 2017 NWPs that remain in effect are:

NWP 1 – Aids to Navigation
NWP 2 – Structures in Artificial Canals
NWP 3 – Maintenance
NWP 4 – Fish and Wildlife Harvesting, Enhancement, and Attraction Devices and Activities
NWP 5 – Scientific Measurement Devices
NWP 6 – Survey Activities
NWP 7 – Outfall Structures and Associated Intake Structures
NWP 8 – Oil and Gas Structures on the Outer Continental Shelf
NWP 9 – Structures in Fleeting and Anchorage Areas
NWP 10 – Mooring Buoys
NWP 11 – Temporary Recreational Structures
NWP 13 – Bank Stabilization
NWP 14 – Linear Transportation Projects
NWP 15 – U.S. Coast Guard Approved Bridges
NWP 16 – Return Water From Upland Contained Disposal Areas
NWP 17 – Hydropower Projects
NWP 18 – Minor Discharges
NWP 19 – Minor Dredging
NWP 20 – Response Operations for Oil or Hazardous Substances
NWP 22 – Removal of Vessels
NWP 23 – Approved Categorical Exclusions
NWP 24 – Indian Tribe or State Administered Section 404 Programs
NWP 25 – Structural Discharges
NWP 27 – Aquatic Habitat Restoration, Establishment, and Enhancement Activities
NWP 28 – Modifications of Existing Marinas
NWP 30 – Moist Soil Management for Wildlife
NWP 31 – Maintenance of Existing Flood Control Facilities
NWP 32 – Completed Enforcement Actions
NWP 33 – Temporary Construction, Access, and Dewatering
NWP 34 – Cranberry Production Activities
NWP 35 – Maintenance Dredging of Existing Basins
NWP 36 – Boat Ramps
NWP 37 – Emergency Watershed Protection and Rehabilitation
NWP 38 – Cleanup of Hazardous and Toxic Waste
NWP 41 – Reshaping Existing Drainage Ditches
NWP 45 – Repair of Uplands Damaged by Discrete Events
NWP 46 – Discharges in Ditches
NWP 49 – Coal Remining Activities
NWP 53 – Removal of Low-Head Dams

NWP 54 – Living Shorelines

2017 NWPs-New Mexico:

The New Mexico Environment Department (NMED), Surface Water Quality Bureau issued conditional WQC for NWPs to ensure that activities conducted under NWPs comply with state water quality standards (New Mexico Administrative Code [NMAC] 20.6.4), Water Quality Management Plan/Continuing Planning Process, including Total Maximum Daily Loads (TMDLs), and Antidegradation Policy.

The NMED denied WQC under all NWPs, except NWP 27, for activities occurring in Outstanding National Resource Waters (ONRW) designated at NMAC, and for NWP 37 for Emergency Watershed Protection and Rehabilitation.

2017 NWPs-Texas:

The Texas Commission on Environmental Quality (TCEQ) issued conditional WQC for the NWPs. The Corps considers WQC for NWP 16 denied.

The Texas Railroad Commission did not provide WQC decision for activities associated with exploration, development, and production of oil, gas or geothermal resources that may result in discharges of pollutants into waters of the United States.  Therefore, the Corps considers WQC waived for these activities.

2017 NWPs-Colorado:

The State of Colorado has mandated by statute that Section 401 water quality certification is issued without additional conditions for all general permits. Please visit the Colorado Department of Public Health and Environment (CDPHE) website for specific information regarding compliance with state water quality certification requirements.

2017 NWPs-Tribal Lands:

Native American Tribes with water quality certifying authority from Environmental Protection Agency (EPA) have the responsibility to make WQC decisions on their lands. The appropriate EPA regional administrator retains the responsibility to make WQC decisions on tribal lands where the tribe does not have this authority from EPA.  EPA Region 8 and 9 provided the following WQC decisions on tribal lands under each region’s responsibility: Region 8 in Colorado; Region 9 for allotted lands within the Navajo Nation.  In New Mexico EPA Region 6 provided WQC for the Pueblo of Zia and Jicarilla Apache Nation and in Texas for Ysleta del Sur.  In New Mexico EPA Region 6 denied WQC for the Pueblos of Jemez, Cochiti, Zuni, San Felipe, Santo Domingo, San Ildefonso, and Mescalero Apache Nation.  As such, applications for individual WQC will need to be submitted to EPA Region 6 before the Corps can provide verification of authorization under a Nationwide Permit.  See the WQC Denials section below for more information. 

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: 

Individual WQC For NWPs:

Applicants seeking verification for a regulated activity under a NWP that has been denied WQC by the CA or seeking authorization within the Section 401 jurisdiction of a CA whose WQC was not accepted by the Corps, MUST obtain an individual WQC or waiver thereof from the appropriate CA [33 CFR 330.4(c)]

Applicants should contact the appropriate CA for more information about how to apply for individual WQC.

For a list of contacts for tribes in the state of New Mexico please consult the Tribal POC list.