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  1. Home
  2. Tribal Programs in the Pacific Southwest
  3. Tribal Clean Water Act Programs
  4. Water Quality Certifications

U.S. Army Corps of Engineers Nationwide Permit Certification Actions

On this page:
  • Background
  • Certification Actions
  • Documents
  • Definitions

Background

This page provides a summary table of the EPA section 401 water quality certification actions for the 57 Nationwide Permits issued by the U.S. Army Corps of Engineers (USACE). These permits and certification actions will expire on March 14, 2026.

EPA Region 9 granted programmatic certification with conditions to 23 of the nationwide permits and denied certification to 9 of the nationwide permits. Project proponents will need to apply for an individual project certification for any nationwide permits that were denied programmatic certification. The remaining 25 nationwide permits either had 401 certification waived or a certification request was not made by the USACE for the permit. Certification letters and conditions as well as definitions are also provided on this page.

The following table includes a summary of Region 9 certification actions on the 57 Nationwide Permits issued by the USACE (note permit numbers 26 and 47 are not used). These permits and certification actions will expire on March 14, 2026.

Certification Actions

EPA Region 9 USACE Nationwide Permit Certification Actions
NWP #NWP NameCertified w/o ConditionsCertified with Applicable Conditions
1Aids to NavigationX 
2Structures in Artificial CanalsX 
3Maintenance 1, 3
4Fish and Wildlife Harvesting, Enhancement, and Attraction Devices and ActivitiesX 
5Scientific Measurement DevicesX 
6Survey ActivitiesX 
7Outfall Structures and Associated Intake Structures 4
9Structures in Fleeting and Anchorage AreasX 
10Mooring BuoysX 
11Temporary Recreational StructuresX 
12Oil or Natural Gas Pipeline Activities 1, 2
13Bank Stabilization 1, 2, 5
14Linear Transportation Projects 1, 2, 3
15U.S. Coast Guard Approved Bridges 3
16Return Water From Upland Contained Disposal Areas 6
17Hydropower Projects 1, 2
18Minor DischargesX 
19Minor DredgingX 
20Response Operations for Oil or Hazardous SubstancesX 
21Surface Coal Mining Activities 1, 2
22Removal of VesselsX 
23Approved Categorical ExclusionsX 
24Indian Tribe or State Administered Section 404 ProgramsWaived 
25Structural DischargesX 
27Aquatic Habitat Restoration, Establishment, and Enhancement Activities 1
28Modifications of Existing MarinasX 
29Residential Developments 1, 2
30Moist Soil Management for WildlifeX 
31Maintenance of Existing Flood Control Facilities 1
32Completed Enforcement ActionsX 
33Temporary Construction, Access, and Dewatering 1, 2
34Cranberry Production ActivitiesWaived 
35Maintenance Dredging of Existing BasinsX 
36Boat RampsX 
37Emergency Watershed Protection and RehabilitationX 
38Cleanup of Hazardous and Toxic WasteX 
39Commercial and Institutional Developments 1, 2
40Agricultural Activities 1, 2, 7
41Reshaping Existing Drainage DitchesX 
42Recreational Facilities 1, 2
43Stormwater Management Facilities 1, 2
44Mining Activities 1, 2
45Repair of Uplands Damaged by Discrete EventsX 
46Discharges in DitchesX 
48Commercial Shellfish Mariculture ActivitiesX 
49Coal Remining Activities 1, 2
50Underground Coal Mining Activities 1, 2
51Land-Based Renewable Energy Generation Facilities 1, 2
52Water-Based Renewable Energy Generation Pilot Projects 1, 2
53Removal of Low-Head Dams 1, 2
54Living ShorelinesX 
55Seaweed Mariculture ActivitiesX 
57Electric Utility Line and Telecommunications Activities 1, 2, 3
58Utility Line Activities for Water and Other Substances 1, 2, 3
59Water Reclamation and Reuse FacilitiesX 
AActivities to Improve Passage of Fish and Other Aquatic Organisms 3

Documents

Free viewers and readers are available to access documents on our website. If you encounter issues with assistive technology, please contact us.

  • EPA Letter to U.S. Army Corps of Engineers South Pacific Division (pdf) (244.03 KB, 2022)
    Programmatic Clean Water Act, Section 401 Certification of the Draft 2021 Nationwide Permits for Tribal Lands within the Region 9 coverage area of the U.S. Environmental Protection Agency.
  • EPA Letter to U.S. Army Corps of Engineers South Pacific Division (pdf) (462.7 KB, 2020)
    Programmatic Clean Water Act, Section 401 Certification of the Draft 2020 Nationwide Permits for Tribal Lands within the Region 9 coverage area of the U.S. Environmental Protection Agency.

Definitions

  • Deny
  • Discharge
  • Grant
  • Grant with Conditions
  • Waive

Deny

States and Tribes deny certification if the activity and discharge will not comply with the applicable sections of the CWA and appropriate requirements of state and Tribal law. The denial of §401 certification by a state or Tribe prohibits the federal agency from issuing the permit or license in question.

Discharge

Under the CWA §401 there does not have to be an actual discharge or a "discharge of a pollutant." The statute states that, "[a]ny…federal license or permit to conduct any activity … which may result in a discharge." Consequently, the discharge need not be a certainty, only that it "may" occur should the permit or license be granted. However, if no discharge may occur, no water quality certification is required. For example, when a RHA §10 permit is required for the hanging of power lines across a navigable river (RHA §10 water) without a potential discharge to the water, the Corps typically has not sought water quality certification.

In addition, the potential discharge does not need to involve an addition of pollutants. Section 401 certification can be triggered not only where there is discharge of a pollutant (such as would be authorized by §402 or §404 permits), but also where there is a discharge not involving addition of a pollutant, such as water released from the tailrace of a dam. As the U.S. Supreme Court has stated, "[w]hen it applies to water, 'discharge' commonly means a 'flowing or issuing out'" and an addition of a pollutant is not "fundamental to any discharge." A lower court has ruled that allowing more water to flow through a dam's turbines is a discharge for §401 purposes.

The third element required for §401 certification to apply is that the potential discharge must be into a water of the U.S. The term "waters of the U.S." is defined in EPA and Corps regulations and applies to all CWA programs. Note, however, that once §401 has been triggered due to a potential discharge into a water of the U.S., additional waters may become a consideration in the certification decision if it is an aquatic resource addressed by "other appropriate provisions of state [Tribal] law."

Grant

The granting of §401 water quality certification to an applicant for a federal license or permit signifies that the certifying authority has determined that the proposed activity and discharge will comply with water quality standards as well as the other identified provisions of the CWA and appropriate requirements of state or Tribal law.

In some circumstances, the provisions states, or Tribes would wish to see reflected in the permit or license can be achieved through early discussions with the applicants, rather than through formally conditioning the 401 certification. For example, incorporation of measures such as the use of Best Management Practices (BMPs) and practices needed for Total Maximum Daily Load (TMDL) implementation are often added to projects during this stage. BMPs can include such actions as using constructed wetlands or bioretention areas rather than retention ponds for catching nutrients and sediments.

Grant with Conditions

The certifying authority may include limitations or conditions in their certifications as necessary to ensure compliance with water quality standards and other provisions of the CWA and appropriate requirements of state or Tribal law.

Waive

A certifying authority may waive §401 certification, either explicitly, through notification to the applicant, or by the certification agency not taking action. If action is not taken on a certification request, "within a reasonable time (which shall not exceed one year)," the state or authorized Tribe has waived the requirement for certification. The amount of time allowed for action on a certification application is determined by the Federal agency issuing the license or permit, while the certifying agency determines what constitutes a "complete application" that starts the timeframe clock. However, the onus for applying for water quality certification lies with the permit or license applicant, and waiver cannot occur without a request for certification.

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Last updated on October 22, 2026
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