Protecting Public Health and the Environment.

National Pollutant Discharge Elimination System Permits

The NPDES program requires facilities discharging from a point source into waters of the U.S. to obtain discharge permits. (A point source is a conveyance such as a pipe or other point.) An NPDES permit contains limits on what can be discharged and other provisions to ensure that the discharge does not harm water quality or the public's health.

There are two basic types of NPDES permits:

  • An individual permit is a permit written specifically for an individual facility.
  • A general permit may cover multiple facilities within one industry, such as aquaculture, or may cover multiple facilities from different industries but that have a similar discharge, such as storm water. General permits are only issued to dischargers within a specific geographical area.

NPDES Program Oversight in Idaho

In Idaho, the NPDES program is administered by EPA, which means EPA is responsible for issuing and enforcing all NPDES permits in Idaho. Idaho is one of only four states that does not administer the NPDES program. The state’s role is to certify that NPDES-permitted projects comply with state water quality standards. Learn more about the certification process.

In 2014, the Idaho Legislature revised Idaho Code to direct DEQ to seek EPA authorization for a state-operated pollutant discharge elimination system permitting program. The state program will be called the Idaho Pollutant Discharge Elimination System (IPDES) program. Learn more.

Aquaculture Facilities

Aquaculture is the cultivating of freshwater fish, such as salmon and trout, under controlled conditions for commercial, conservation, and recreation uses. EPA has issued a general NPDES permit for aquaculture facilities and associated fish processing facilities in Idaho. Learn more.

Concentrated Animal Feeding Operations (CAFOs)

The Clean Water Act defines concentrated animal feeding operations, also called "CAFOs" or "feedlots," as point sources; therefore, they are subject to NPDES permitting. Animal waste and wastewater can enter water bodies from spills or breaks of waste storage structures and non-agricultural application of manure to crop land. EPA has proposed a general NPDES permit for CAFOs in Idaho. Learn more.

Wastewater Treatment Plants

Wastewater treatment plants collect wastewater (mainly domestic sewage) and may discharge treated wastewater into waters of the Unites States with an NPDES permit. The permits include provisions relating to biosolids; permits for municipal facilities may also specify pretreatment requirements for industries that discharge their wastewater to the wastewater treatment plants. EPA uses the term "publicly owned treatment works" to describe municipal wastewater treatment plants.

Biosolids (Sewage Sludge)

Biosolids are the nutrient-rich organic materials resulting from the treatment of sewage sludge (the solid, semisolid, or liquid untreated residue generated during the treatment of domestic wastewater [sewage]). Biosolids can be safely recycled and applied as fertilizer.

A biosolids permit is required for wastewater treatment plants that treat domestic sewage and is issued as part of the facility's NPDES permit. Other types of industries may work with biosolids or apply biosolids as fertilizer and may not be required to obtain a biosolids permit (always check with EPA to be sure). However, those who work with biosolids must comply with federal biosolids regulations even when a permit is not required.

In addition to federal regulations, Idaho has its own state rules that regulate the use of sewage sludge (biosolids) (IDAPA, Sludge Usage). These rules require land appliers of domestic sewage sludge to submit a sludge disposal plan to DEQ or obtain approval on a site-by-site basis. DEQ must approve the plan before the sludge can be land applied. Learn more.


The National Pretreatment Program is a portion of the NPDES program established to address discharges from industries to wastewater treatment plants. The program requires industrial and commercial dischargers to treat ("pretreat") or control pollutants in their wastewater prior to discharge to wastewater treatment plants. It is the wastewater treatment plant's NPDES permit that specifies pretreatment requirements. Industrial users must comply with the pretreatment standards and reporting requirements.


Stormwater is water from rain or melting snow that does not immediately soak into the ground. Stormwater runs off of land and hard surfaces such as streets, parking lots, and rooftops, and picks up pollutants, such as fertilizers, dirt, pesticides, and oil and grease. Eventually, stormwater soaks into the ground or discharges to surface water (usually through storm drains), bringing the pollutants with it. Most stormwater discharges are considered point sources and require coverage by an NPDES permit. Construction activities, certain industries, and municipal separate storm sewer systems (MS4s) are all required to have stormwater permits. Like the rest of the NPDES program, the NPDES stormwater program in Idaho is operated by EPA. Learn more.

Staff Contacts

401 Program Coordinator
Loren Moore
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0158

Wastewater Engineering Manager
Larry Waters
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0151

IPDES Program Manager
Mary Anne Nelson
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0291

DEQ Resources

More Information on EPA's Website

Related Pages

§401 Certification

§401 Certifications: NPDES Permits