US Army Corps of Engineers
Albuquerque District Website Website

Water Quality Certification

Under Section 401 of the Clean Water Act, certification of compliance with state or tribal water quality standards by the state/tribal water quality certifying authority is required for any discharge of dredged/fill material into water of the United States under Section 404 of the Act (see 33 CFR 325.2 [Individual Permits] and 33 CFR 330.4(c) [Nationwide Permits]). The Environmental Protection Agency (EPA) administers Section 401 Water Quality Certification (WQC) for tribes that do not have water quality certifying authority.


WQC for Nationwide Permits (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.


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.



The State of Colorado has mandated by statute that Section 401 water quality certification is issued without 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.

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:



WQC Denials:

In accordance with Corps regulations at 33 CFR 330.4(c), denial of WQC for activities authorized by the NWPs also results in the Corps denying authorization under a NWP for those activities without prejudice.  Anyone wanting to perform Clean Water Act, Section 404 regulated activities under a NWP must first obtain an individual WQC or waiver thereof from the appropriate WQC authority and must submit a pre-construction notification to the Corps Albuquerque District.  Clean Water Act, Section 401(a)(1) requires certifying authorities to establish public notice procedures for all individual WQCs.  The Corps will not require or process an individual permit application for an activity which may result in a discharge and otherwise qualifies for an NWP solely on the basis that the WQC has been denied for that NWP.  Also, in accordance with Corps regulations at 33 CFR 330.4(c)(6), the Corps will presume WQC is waived if a decision has not been issued by the WQC authority within 60 calendar days from the receipt of an individual WQC application and verification of authorization under a NWP will be provided to the permittee.

Applicants should contact the appropriate WQC authority 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.


WQC for Standard Individual Permits (IPs)

New Mexico & Tribal Lands:

For all activities that require an IP, applicants must either submit an application to the NMED, to the tribes listed above, or to the EPA for tribes not listed above to obtain Individual WQC.


The TCEQ and the Corps developed a tiered system of review for all IP applications based on project size and the area of waters affected. Generally, for small projects (Tier I) that affect less than three acres of waters in the state, or less than 1,500 linear feet of streams, TCEQ has determined that incorporating certain Best Management Practices (BMPs) and other requirements into the project will sufficiently protect water quality. Any project that does not qualify for a Tier I review, or for which the applicant elects not to incorporate Tier I criteria, or prefers to use alternatives, will be considered a Tier II, which is subject to a certification review by TCEQ. Please note that completion of a questionnaire is not required in order for a Section 404 application to be considered administratively complete by the Corps, but is required for the TCEQ to process a request for WQC. If the project qualifies for Tier I, then the applicant must complete the required BMPs form and submit it to TCEQ. If the project does not qualify for Tier I, if the applicant is unable to follow the BMPs, or if the applicant chooses not to follow the Tier I requirements, then the applicant must complete and submit the Section 401 certification questionnaire and the alternatives analysis checklist to TCEQ.

TCEQ State Water Quality Certification of Section 404 Permits


The Colorado Department of Public Health and Environment (CDPHE) authorizes WQC for activities in the State of Colorado. Applicants must submit an application to the CDPHE for Individual WQC.  The state of Colorado has established submittal requirements for projects applicable to the provisions of the Colorado 401 certification process.