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Water Quality Certifications for Projects Requiring a Federal Permit

Regulated Activities

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 (WQC) is issued, verifying compliance with state water quality requirements. In New York State, applicants for a Federal license or permit for activities that may result in a discharge into waters of the United States are required to apply for and obtain a WQC from DEC indicating that the proposed activity will comply with New York State water quality standards.

A WQC from DEC is most commonly required when a project also requires a permit from the U.S. Army Corps of Engineers under Section 404 of the CWA for the placement of fill in waters of the United States. Some examples of activities requiring a WQC are:

  • Streambank & lake shoreline stabilization
  • Bridge & culvert installations and repair
  • Dredging in navigable waters
  • Road and driveway construction in wetlands or streams
  • Temporary construction access in wetlands or streams

Application Procedures

To comply with United States Environmental Protection Agency rules, effective September 11, 2020 concerning Water Quality Certifications, a pre-filing meeting request must be sent to DEC at least 30 days prior to applying. The request can be completed by using the pre-filing meeting request form (PDF), which must be sent along with the supporting attachments to the appropriate DEC Regional Permit Administrator.

Requirements for a WQC application include the Joint Application Form (PDF), the WQC-1 Form Supplement (PDF), and additional materials as appropriate. For more information, please see Environmental Permits Forms and Requirements.

Blanket Coverage

Certain activities have already been provided blanket statewide WQC and do not require an individual determination. The DEC Blanket Water Quality Certification, only applies to limited activities, and those that are covered by a specific U.S. Army Corps of Engineers Nationwide 404 Permit.

In 2020 the Corps of Engineers proposed to reissue and modify all of the 2017 Nationwide Permits. However, after the completion of the public notice process the Corps of Engineers only proceeded to reissue and modify some of the Nationwide Permits, which became effective March 15, 2021. Those nationwide permits were subject to DEC Blanket Water Quality Certification issued on December 18, 2020.

Since December 18, 2020, the Corps of Engineers proposed to finalize the remaining Nationwide Permits and provided DEC until October 15, 2021 to revise its blanket WQC decision for those remaining permits. DEC issued a revised blanket Water Quality Certification on October 15, 2021 for the remaining permits. Effective February 25, 2022, the Corps of Engineers finalized the remaining Nationwide Permits.

As a result, there are currently two sets of U.S. Army Corps of Engineers Nationwide 404 Permits in effect, some in effect since March 15, 2021 and some in effect since February 25, 2022. The DEC blanket WQC decision issued October 15, 2021 (PDF) addresses both sets of Nationwide Permits. However, those Nationwide Permits effective March 15, 2021 are subject to conditions and limitations set by DEC on December 18, 2020 (Attachments 1, 2, and 3 of the October 15, 2021 decision letter) and those Nationwide Permits effective February 25, 2022 are subject to conditions and limitations set by DEC on October 15, 2021 (Attachments 1, 2, and 5 of the October 15, 2021 decision letter).

The following table indicates which Corps of Engineers' Nationwide Permits are covered by which set of DEC blanket WQC conditions:

Nationwide Permit (NWP) No. and Title Applicable DEC Blanket WQC Decision
December 18, 2020 October 15, 2021
NWP 1 Aids to Navigation WQC Not Required
NWP 2 Structures in Artificial Canals WQC Not Required
NWP 3 Maintenance Issued w/Conditions


Fish and Wildlife Harvesting, Enhancement, and Attraction Devices and Activities Issued w/Conditions
NWP 5 Scientific Measurement Devices Issued w/Conditions
NWP 6 Survey Activities Issued w/Conditions
NWP 7 Outfall Structures and Associated Intake Structures Issued w/Conditions
NWP 8 Oil and Gas Structures on the Outer Continental Shelf WQC Not Required
NWP 9 Structures in Fleeting and Anchorage Areas WQC Not Required
NWP 10 Mooring Buoys WQC Not Required
NWP 11 Temporary Recreational Structures WQC Not Required
NWP 12 Oil or Natural Gas Pipeline Activities Denied**
NWP 13 Bank Stabilization Issued w/Conditions
NWP 14 Linear Transportation Projects Issued w/Conditions
NWP 15 U.S. Coast Guard Approved Bridges Issued w/Conditions
NWP 16 Return Water from Upland Contained Disposal Areas Denied
NWP 17 Hydropower Projects Denied
NWP 18 Minor Discharges Issued w/Conditions
NWP 19 Minor Dredging Issued w/Conditions
NWP 20 Response Operations for Oil or Hazardous Substances Issued w/Conditions
NWP 21 Surface Coal Mining Activities Denied
NWP 22 Removal of Vessels Issued w/Conditions
NWP 23 Approved Categorical Exclusions Issued w/Conditions
NWP 24 Indian Tribe or State Administered Section 404 Programs WQC Not Required
NWP 25 Structural Discharges Issued w/Conditions
NWP 26 Reserved
NWP 27 Aquatic Habitat Restoration, Establishment, and Enhancement Activities Issued w/Conditions
NWP 28 Modifications of Existing Marinas WQC Not Required
NWP 29 Residential Developments Issued w/Conditions
NWP 30 Moist Soil Management for Wildlife Issued w/Conditions
NWP 31 Maintenance of Existing Flood Control Facilities Issued w/Conditions
NWP 32 Completed Enforcement Actions Issued w/Conditions
NWP 33 Temporary Construction, Access, and Dewatering Issued w/Conditions
NWP 34 Cranberry Production Activities Issued w/Conditions
NWP 35 Maintenance Dredging of Existing Basins WQC Not Required
NWP 36 Boat Ramps Issued w/Conditions
NWP 37 Emergency Watershed Protection and Rehabilitation Issued w/Conditions
NWP 38 Cleanup of Hazardous and Toxic Waste Denied
NWP 39 Commercial and Institutional Developments Issued w/Conditions
NWP 40 Agricultural Activities Issued w/Conditions
NWP 41 Reshaping Existing Drainage Ditches Issued w/Conditions
NWP 42 Recreational Facilities Issued w/Conditions
NWP 43 Stormwater Management Facilities Issued w/Conditions
NWP 44 Mining Activities Denied
NWP 45 Repair of Uplands Damaged by Discrete Events Issued w/Conditions
NWP 46 Discharges in Ditches Issued w/Conditions
NWP 47 Reserved
NWP 48 Commercial Shellfish Mariculture Activities Issued w/Conditions
NWP 49 Coal Re-mining Activities Denied
NWP 50 Underground Coal Mining Activities Denied
NWP 51 Land-Based Renewable Energy Generation Facilities Issued w/Conditions
NWP 52 Water-Based Renewable Energy Generation Projects Denied
NWP 53 Low-Head Dam Removal Denied
NWP 54 Living Shorelines Denied
NWP 55 Seaweed Mariculture Activities WQC Not Required
NWP 56 Finfish Mariculture Activities WQC Not Required
NWP 57 Electric Utility Line and Telecommunications Activities Issued w/Conditions
NWP 58 Utility Line Activities for Water and other Substances Issued w/Conditions
**Projects require individual water quality certification from DEC where blanket water quality certification has been denied.

For more information regarding the US Army Corps of Engineers Nationwide 404 Permits, please contact the appropriate Office:

Early in the development of a project proposal it may be difficult to determine whether proposed activities are covered under a Corps of Engineers Nationwide Permit and DEC Blanket WQC. As a result, individuals are encouraged to contact the appropriate Corps of Engineers District office and DEC Regional Permit Administrator for guidance before undertaking work.

Is Your Project Minor or Major?

Application review time frames, procedures, and requirements for public notice differ for Minor and Major projects under the Uniform Procedures Act requirements (6NYCRR Part 621). Generally, Minor projects have shorter review time frames and require less public review.

Minor Water Quality Certification projects include those projects which will not exceed the Minor project thresholds for Protection of Waters, Freshwater Wetlands, or Tidal Wetlands Permits, and which do not involve the approval of construction and operation of hydroelectric generating facilities. All other projects are considered Major.

For additional information see our web page Getting an Environmental Permit.

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