Protecting Public Health and the Environment.


Municipalities in Idaho may have one or more activities that require permits from DEQ under the IPDES Program. Cities with wastewater treatment plants that discharge into a water of the United States in Idaho must obtain an individual IPDES permit. Those cities that operate a municipal separate storm sewer system (MS4) may also require coverage under the general permit for MS4s. Cities that have industrial users subject to pretreatment standards may either need pretreatment programs approved by DEQ or be required to develop programs for approval.

Other publicly owned entities such as sewer districts or authorities that operate wastewater treatment plants or storm sewer systems are also required to have an IPDES permit for any discharges into a water of the United States. Privately owned treatment works treating domestic sewage and discharging to a waters of the United States in Idaho are also required to obtain an IPDES permit. These privately owned treatment works will not be transferred to Idaho authority until July 1, 2019.

The following processes and procedures provide information about the process operators of publicly and privately owned treatment works should follow to apply for the necessary IPDES permits.

Application and Processing Procedures

Operators of publicly and privately owned treatment works are encouraged to schedule a preapplication meeting with DEQ to describe the facility or activity and discuss the wastewater management alternatives offered by the state. If a surface water discharge is deemed the most appropriate avenue to pursue, DEQ will explain the permitting process and estimated permit issuance date.

Applications submitted to DEQ must be conducted via DEQ’s E-Permitting system. DEQ’s E-Permitting system helps the operator submit the necessary information to ensure that an application for an IPDES permit is completed in a timely manner. After receiving the application, DEQ reviews the information submitted to ensure all required information and data are provided. DEQ will issue a completeness determination within 30 days for new dischargers and 60 days for renewal applicants. 

Operators of wastewater treatment facilities apply for an individual permit for the discharge activity. All individual permits follow the same process for development and issuance. Every IPDES facility will be assigned to a permit writer who will be responsible to 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

All permits require permittees to properly maintain and operate their treatment, control, and monitoring equipment; respond to DEQ’s requests for relevant information; provide access to the permitted facility to inspect equipment, operations, and records and to monitor compliance; and report information pertaining to planned physical or operational changes and noncompliance episodes. Failure to comply may result in civil penalties and permit revocation. IPDES permits are issued for a term not to exceed 5 years. Before the permit expires, the permittee must submit a renewal application.

Specific Permit Conditions

Each facility has unique environmental conditions, wastewater compositions, and operation. Each IPDES 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; pretreatment requirements; and the physical, chemical, and biological characteristics of the wastewater. Varying compliance schedules as well as monitoring and reporting requirements may be imposed.

Drinking Water Treatment

Drinking water treatment facilities that discharge to waters of the United States in Idaho also need to obtain an IPDES permit for the discharge activity. Drinking water treatment facilities may apply for coverage under an IPDES permit for backwash water, reject water, and miscellaneous wastewater disposal for processes using filter backwash, filter-to-waste, thickener overflows (supernatant), decant water, and from miscellaneous waste streams. Potable water treatment facilities not covered by the general permit include batch regenerated potassium permanganate iron removal, sodium zeolite softening and ion exchange or reverse osmosis units. Drinking water treatment facilities using these technologies must apply for an individual discharge permit instead of seeking coverage under the general permit.

Applying for coverage under the general permit requires the operator to submit a notice of intent for coverage via DEQ’s E-Permitting system. The drinking water treatment general permit will transfer to DEQ’s authority on July 1, 2020. Operators of these systems will not need to file a new notice of intent with DEQ upon transfer. Operators of these systems will need to renew their notice of intent in accordance with the timelines described in permit IDG380000. All facilities intending to continue discharging beyond the permit expiration date must submit an NOI for continued coverage at least 180 days before the expiration date of the permit.


DEQ’s pretreatment program will be essentially the same as the federal program established in 40 CFR 403 and adopted by reference in IDAPA The objectives for the pretreatment program are as follows:

  • Prevent the introduction of pollutants into a POTW that will interfere with the operation of the POTW, including interference with the use or disposal of sewage sludge.
  • Prevent the introduction of pollutants into a POTW that will pass through the treatment works or otherwise be incompatible with the works.
  • Improve the opportunities to recycle and reclaim municipal and nonmunicipal wastewater and sewage sludge.

 Learn more about the IPDES Pretreatment Program here.

Municipal Separate Storm Sewer Systems (MS4)

Storm water runoff is often controlled by municipalities, or other public entities like highway districts, to ensure that infrastructure and population are protected from unmitigated runoff. When a city has a storm sewer system that is separate from its wastewater collection system and meets certain size criteria [GET LINK TO MS4 CRITERIA DOCUMENT], the city may need to have coverage for the system’s discharge to the surface water. To prevent harmful pollutants from being washed or dumped into MS4s, storm water management programs may be required that describe the control practices the city will implement. 

Learn more about municipal storm water permitting here.


Staff Contacts

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

IPDES Municipal Permit Writer
Lauri Monnot
DEQ State Office
Water Quality Division
1410 N. Hilton
Boise, ID 83706
(208) 373-0203

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)

Idaho Pollutant Discharge Elimination System: User's Guide to Permitting and Compliance Volume 2—Publicly Owned Treatment Works (December 2017)

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