Protecting Public Health and the Environment.

Industrial Dischargers

Wastewater discharges from industrial sources contain pollutants at levels that affect the quality of receiving waters or interfere with publicly owned treatment works (POTWs) that receive those discharges. IPDES permits establish discharge limits and conditions for industrial sources with specific limits based on the type of facility or activity generating the discharge.

Industrial dischargers that connect to a publicly or privately owned treatment works are regulated under the pretreatment program.

Individual Permits

Industrial wastewater discharges refer to categories of new or existing direct discharges of process or nonprocess water from manufacturing, commercial, mining, silvicultural activities, or drinking water treatment operations (public and private).

On July 1, 2019, authority for individual industrial permitting will transfer to DEQ. To apply for an individual industrial permit, use the IPDES E-Permitting system.

Application and Processing Procedures

Anyone conducting an activity that requires a permit is encouraged to schedule a preapplication meeting with DEQ to describe the facility or activity and discuss the wastewater discharge alternatives offered by the state. If surface water discharge is deemed the most appropriate avenue to pursue, DEQ will guide the applicant through the permitting process.

The operator will use DEQ’s E-Permitting system to provide necessary application information. Upon receiving the application, DEQ will review the information submitted to ensure all requirements have been met. DEQ will issue a completeness determination within 30 days for new dischargers and 60 days for renewal applicants.

Industrial facilities are typically required to apply for individual permits for their wastewater discharge activities. All individual permits follow the same process for development and issuance, except that an application for a new or substantially modified industrial facility will include a new source determination review. Every IPDES facility will be assigned to a permit writer who will determine application completeness, determine whether DEQ should deny or issue a permit, compose the draft permit and fact sheet, navigate the documents through the public comment process, and issue or reissue the permit.

Standard Permit Conditions

Standard permit conditions are included in all permits and describe the conditions applicable to all permits to which permittees must comply as outlined in IDAPA Failure to comply may result in civil penalties and permit revocation. IPDES permits are issued for a term of 5 years, and the permittee is responsible for applying for a new permit in a timely manner to continue operation.

Specific Permit Conditions

Each facility has unique environmental conditions, wastewater compositions, and operation. Each IPDES individual permit is developed to address the unique conditions specific to the wastewater facility and the surface water receiving the discharge. The permit writer reviews the specific facility conditions, the environmental conditions, and any other condition relevant to the type of treatment operations.

Specific permit conditions differ from facility to facility and may specify or limit wastewater composition; the method, manner, and frequency of wastewater discharge; and the physical, chemical, and biological characteristics of the wastewater. Varying compliance schedules as well as monitoring and reporting requirements may be imposed as well.


No application fee is required for an individual industrial permit; however, an annual fee for an IPDES individual industrial permit will be assessed and invoiced based on the fee schedule found at IDAPA beginning July 1, 2020. Payment of the fee is expected by October 1, 2020 and by October 1 of subsequent years.

Permit Type

Annual Fee

Major Individual Industrial


Minor Individual Industrial


General Permits

DEQ may issue a general permit when discharges within a distinct geographic area (e.g., statewide or regional) involve the same or substantially similar types of operations; discharge the same types of wastes; and require the same effluent limits, monitoring, or operating conditions. General permits are a cost-effective option because a large number of facilities can be covered under a single permit.

General permits for the following classes of industrial discharges will be issued by DEQ:

  • Concentrated animal feeding operations (CAFOs)
  • Concentrated aquatic animal production (CAAP) facilities
  • Pesticide applications
  • Ground water remediation activities
  • Small suction dredge placer mining
  • Hydroelectric projects
  • Storm water for industrial and construction activities

Transfer of authority for general permits, other than storm water, will occur July 1, 2020. Until then, requests for coverage under the general permits listed above must occur via EPA’s eNOI system, a free online service. To submit an NOI, update your NOI, submit your annual report, or submit an NOT before July 1, 2020. Visit Central Data Exchange (CDX) to use the eNOI System.


EPA developed a user’s guide to walk decision makers through the process of submitting NOIs, NOTs, and annual reports.


CAFOs are agricultural facilities that house and feed a large number of animals in a confined area for 45 days or more during any 12-month period. These animals typically include cows, hogs, chickens, or turkeys. Animal waste and facility-generated wastewater can enter water bodies from spills or breaks of waste storage structures and nonagricultural application of manure to crop land. The Clean Water Act defines CAFOs as point sources; therefore, they are subject to IPDES permitting.

Aquaculture IPDES Permits

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

In Idaho, a general IPDES permit offers coverage for aquaculture facilities and associated fish processing facilities in Idaho. The permit authorizes discharges from facilities engaged in growing, containing, or holding 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. Approximately 115 permitted operations exist in Idaho, nearly 70% 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.

Pesticide Applications

The NPDES permitting program, under the Pesticide General Permit (PGP), regulates discharges from pesticide applications. Point source discharges of biological pesticides and chemical pesticides that leave a residue into waters of the United States are required to comply with NPDES requirements. The PGP offers coverage for pesticide operators. Activities not eligible for coverage under the PGP may be eligible for coverage under an individual permit.

Ground Water Remediation Activities

Discharges authorized by the ground water remediation general permit include facilities that extract contaminated ground water from the subsurface and treat it in an aboveground system for both petroleum- and nonpetroleum-related cleanups. The majority of discharges covered contain one or more pollutants from common chemical groups such as suspended solids, total petroleum hydrocarbons, other volatile organic compounds, polycyclic aromatic hydrocarbons, semivolatile compounds, and metals. This general permit does not authorize emergency response actions pursuant to the National Oil and Hazardous Substances Pollution Contingency Plan, facilities operating as part of an on-site response action conducted pursuant to the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA), mining operations, and facilities discharging treated ground water to a sanitary sewer under an authorized pretreatment program.

Small Suction Dredge Placer Miners

A suction dredge is an underwater system that pulls up streambed material through a suction hose and runs it across a recovery system floating at the surface. Gold pieces are separated from other streambed materials and trapped as gravel and other materials wash through the system and discharge back into the stream. Owners or operators of suction dredges covered by the Idaho Department of Water Resources Idaho Recreational Mining Authorization may be eligible for coverage under this general permit. The small suction dredge placer mining general permit authorizes discharges from small suction dredge operations with intake nozzle diameters of less than or equal to 5 inches or the diametrical equivalent and a cumulative rating of 15 horsepower or less.

NOIs for coverage under this general permit should be submitted to EPA’s Idaho Operations Office in Boise. More information on the NOI requirements is available in the general permit.

Hydroelectric Projects

EPA is drafting a general permit to cover discharges from hydroelectric generating facilities including equipment cooling water, equipment and floor drain water, equipment backwash strainer water, and specific maintenance waters from the hydroelectric facility. Pollutants associated with these wastewaters include oil, grease, excess heat, pH, and backwash water from cleaning river debris and silt from the strainer’s screen.

Submit NOIs for coverage under this general permit to EPA’s Idaho Operations office and DEQ. More information on the NOI requirements will be available in the general permit when EPA publishes it for public comment or issues the final permit.

Storm Water for Industrial and Construction Activities

Storm water results from rain or melting snow that does not immediately soak into the ground. Storm water 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, storm water soaks into the ground or discharges to surface water (usually through storm drains), bringing the pollutants with it. Most storm water discharges are considered point sources and require coverage by an IPDES permit. Construction activities, certain industries, and municipal separate storm sewer systems are all required to have storm water permits.

More information on storm water permitting can be found here.

Staff Contacts

IPDES Permit Supervisor
AJ Maupin
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0167

IPDES Industrial Permit Writer
Rakael Pope
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0599

DEQ Resources

E-Permitting for POTWs

Electronic Reporting Waiver - Note: This form opens best in Internet Explorer. For Mozilla Firefox users, you may get a “Please Wait” message and will need to click on the “Open with Different Viewer” prompt on the top right of the screen if the document does not display properly. If this form does not open, download it to your desktop.

Electronic Reporting Waiver Policy

NetDMR | NetDMR Instructions

More Information

Idaho Pollutant Discharge Elimination System: User's Guide to Permitting and Compliance Volume 1 — General Information (April 2017)

Approval of Statewide NPDES Program (Idaho Code: Title 39, Chapter 1, Section 39-175C)