Protecting Public Health and the Environment.

Aquaculture NPDES Permits

Aquaculture is the cultivating of freshwater fish, such as salmon and trout, under controlled conditions for commercial, conservation, and recreation uses.

Aquaculture operations in Idaho are regulated by the National Pollutant Discharge Elimination System (NPDES), a permitting system for wastewater discharges under the federal Clean Water Act. NPDES permits set limits on the types and amounts of pollutants that industries and municipalities can release into the nation's waterways.  

In Idaho, the NPDES permitting program is administered by EPA. EPA has issued a general NPDES permit for aquaculture facilities and associated fish processing facilities in Idaho. The permit authorizes discharges from facilities engaged in the growing, containing, or holding of fish in ponds, raceways, and other similar structures. The hatcheries and fish farms permitted under the Idaho general permit include state, federal, tribal, and private facilities. There are approximately 115 permitted operations in Idaho, nearly 70% of which operate in the Magic Valley, discharging to the Snake River or its tributaries.

To be covered under the general permit, a facility must develop a best management practices plan as outlined in the Idaho Waste Management Guidelines for Aquaculture Operations and submit a permit application to EPA.

DEQ's Role

DEQ issues §401 water quality certifications as part of the NPDES permitting process. A §401 certification states that any discharge will comply with the Clean Water Act and will not cause an exceedance of state water quality standards. DEQ also performs NPDES inspections of aquaculture facilities under contract with EPA. DEQ staff review plans and specifications for aquaculture waste treatment systems and provide technical assistance to aquaculture facility operators regarding waste management practices.

Staff Contacts

Aquaculture Coordinator
DEQ Twin Falls Regional Office
650 Addison Avenue West, Suite 110
Twin Falls, ID 83301
(208) 736-2190

More Information

EPA's General Permit for Idaho Aquaculture Facilities and Associated Fish Processing Facilities

Final §401 Water Quality Certification of EPA's Aquaculture Facilities General Permit

Related Pages

Aquaculture in Idaho

§401 Certification