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Water Quality Certification

Protecting surface water quality and uses by ensuring compliance with state water quality standards.

The purpose of the Water Quality Certification (WQC) program is to protect surface water quality and uses (such as swimming and aquatic life) by ensuring compliance with New Hampshire surface water quality standards. Examples of surface waters include lakes, ponds, rivers, streams, wetlands and tidal waters. The WQC program is authorized by New Hampshire RSA 485-A:12, III and IV. Water Quality Certification for federal National Pollutant Discharge Elimination System (NPDES) permits are administered by the NHDES Wastewater Engineering Bureau. All other WQCs are administered by the NHDES Watershed Management Bureau. Water Quality Certifications typically include enforceable conditions, including monitoring requirements, to ensure compliance with surface water quality standards.

Who is required to apply for water quality certification?

Water quality certification is required for any activity that requires certification under §401 of the federal Clean Water Act as well as for any surface water withdrawal or diversion that requires registration under RSA 488-A:3 and was not in active operation as of September 5, 2008. §401 of the CWA requires that, for any federally-licensed or permitted project that may result in a discharge into waters of the United States (33 USC 1341), a water quality certification be issued to ensure that the discharge complies with applicable water quality requirements or that certification be waived. EPA's regulations at 40 CFR 121 (PDF) address §401 certification generally. EPA also has water quality certification regulations for federally-issued CWA Section 402 permits that are subject to the Section 401 certification requirements (40 CFR 124.53-124.55). Other federal agencies may also have §401 certification regulations for their licensing and permitting programs. Activities that are covered under general federal permits such as the U.S. Army Corps of Engineers §404 general permits for New Hampshire do not need to submit an application for water quality certification unless notified by the NHDES.

How Do I Apply?

To submit an application, go to the Application for Water Quality Certification

§401 WQC applications should be sent by email to James Tilley at A hardcopy with original (wet) signatures and dates should also be sent by mail to the following address:

Attn: James Tilley, Watershed
NH Department of Environmental Services 
29 Hazen Drive, P.O. Box 95
Concord, New Hampshire 03302-0095

Am I required to hold a pre-application meeting?

Prior to submitting a §401 WQC application, we recommend that applicants contact NHDES (see contact information at the bottom of this webpage) to discuss the project and application requirements, and if necessary, schedule a meeting.
(EPA’s 2020 Clean Water Act Section 401 Certification Rule (40 CFR Part 121), which was in effect from September 11, 2020 to October 21, 2021, required applicants applying for §401 Water Quality Certification to request a pre-application meeting with NHDES at least 30 days prior to submitting a certification request. However, on October 21, 2021, the U.S. District Court for the Northern District of California issued an order remanding and vacating EPA’s 2020 Clean Water Act Section 401 Certification Rule the 2020 Rule. The order requires a temporary return to EPA’s 1971 Rule until EPA finalizes a new certification rule, which does not require a pre-application meeting.)

How long does the application process take?

The time needed for NHDES to act on a certification can take from approximately 60 days to no more than one year depending on the federal license or permit being sought, and the complexity of the project. Draft certifications are typically posted on the NHDES website for a minimum 30-day public comment period prior to NHDES rendering a final decision.

Tools and Guidance
Rules and Regulations
Water Quality Certification Program Supervisor