Protecting Public Health and the Environment.

§401 Certification

Section 401 of the federal Clean Water Act requires state certification for any permit or license issued by a federal agency for an activity that may result in a discharge into waters of the U.S. This requirement allows each state to have input into federally approved projects that may affect its waters (rivers, streams, lakes, and wetlands) and to ensure the projects will comply with state water quality standards and any other water quality requirements of state law. Any §401 certification in Idaho also ensures that the project will not adversely impact impaired waters (waters that do not meet water quality standards) and that the project complies with applicable water quality improvement plans (total maximum daily loads).

DEQ is responsible for issuing §401 certifications in Idaho for the following types of federal permits or licenses:

  • National Pollutant Discharge Elimination System (NPDES) Permits: The NPDES program requires facilities discharging from a point source such as a pipe into waters of the US to obtain discharge permits. EPA has authorized the transfer of permitting authority to the Idaho Pollution Discharge Elimination System (IPDES) Program and the phased transfer of permits will lead to IPDES issuance of all discharge permits by July 1, 2021. Learn more.
  • §404 Dredge and Fill Permits: The federal Clean Water Act requires a permit to conduct water-related construction activities, such as fills for development, water resource projects, and infrastructure development. The US Army Corps of Engineers is responsible for issuing dredge and fill permits in Idaho. Learn more.
  • Hydroelectric Power Plants: State certification is required before the Federal Energy Regulatory Commission (FERC) may license or relicense nonfederal hydroelectric dams. Learn more.

How Does the §401 Certification Process Work?

DEQ must grant, deny, or waive §401 certification for a project before a federal permit or license can be issued. Depending on the type of project, the applicant applies for §401 certification directly with DEQ or applies for a federal permit with the appropriate federal agency and that agency requests the certification from DEQ. DEQ must act on a request for certification within a reasonable period of time, which cannot exceed one year, after which the certification requirement will be waived.

DEQ can waive certification (either expressly or by taking no action), deny the certification, grant the certification, or grant the certification with conditions. It is unusual for DEQ to waive a certification; however, if a certification is waived, the federal agency may still issue the permit or license.

It is also unusual for DEQ to deny a certification, as DEQ generally works closely with the federal agency issuing the permit or the applicant applying for the permit or license to ensure that the project can be certified to meet Idaho's water quality standards. However, a certification may be denied if there is no reasonable assurance the activity can proceed and meet water quality standards. If DEQ denies the certification, the federal agency cannot issue the license or permit. Depending on the circumstances, DEQ may deny the certification without prejudice, which allows the applicant to request certification again after amending the application. DEQ may choose this route when not enough information was provided to give the required assurance of compliance with water quality standards.

When a certification is issued with conditions, it may specify effluent or other limitations and/or other requirements (e.g., monitoring, reporting, implementing best management practices) to ensure the project will not violate state water quality standards or other water quality requirements of state laws. Those conditions become conditions of the license or permit and are enforceable.

DEQ's final certification decisions can be appealed, as provided by the Idaho Environmental Protection and Health Act and the Idaho Administrative Procedure Act. The appeal is a prerequisite to any court action. The procedures and timelines DEQ follows when issuing state §401 water quality certification decisions are outlined in Idaho's §401 certification guidance.

Applying for §401 Certification

EPA and the US Army Corps of Engineers work with DEQ to obtain certification for NPDES permits and §404 dredge and fill permits. Only companies applying for §401 certification of FERC licenses need to apply directly with DEQ. Whether an applicant applies directly with DEQ or through a federal agency, the applicant needs to include sufficient information to provide reasonable assurance that the project will comply with the Clean Water Act and meet state water quality standards. Following are examples of the type of information DEQ needs to make a decision:

  • Legal name and address of activity owner or operator
  • Legal name and address of owner or operator's authorized representative
  • Names of water bodies impacted by the project
  • Complete written description of activity, including maps, diagrams, and other information
  • Description of water quality impacts from the existing activities and proposed activities
  • Identification of measures to prevent or mitigate violations or contributions to violations of water quality standards
  • Copies of environmental information submitted to the federal licensing or permitting agency

DEQ does not charge a fee for §401 certifications.

§401 Certification Decisions

Access to the status of §401 certification decisions in Idaho, including certifications of general and individual NPDES permits and nationwide, regional general, and individual dredge and fill permits is provided via this website.

Hells Canyon Complex Project

A number of hydroelectric facilities in Idaho are in or soon will be in the process of obtaining new licenses, including the large Hells Canyon Complex (Brownlee, Oxbow, and Hells Canyon Dams). DEQ is currently reviewing a water quality certification application for this project. Learn more.

Bear River Narrows Hydroelectric Project

Twin Lakes Canal Company has proposed building a dam on the Bear River in Franklin County. The 109-foot-tall dam would create a 4.5-mile-long reservoir in the Oneida Narrows Canyon with a storage capacity of 12,647 acre-feet. DEQ is required to make a certification decision within a year’s timeframe from the January 14, 2015, request for certification. Learn more.

Staff Contacts

401 Program Lead
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706

DEQ Resource

§401 Certification Guidance (September 2012)

More Information

Water Quality and 401 Certification

Related Pages

§401 Certifications: Dredge & Fill

§401 Certifications: NPDES Permits