Idaho Pollutant Discharge Elimination System (IPDES) permits authorize the discharge of pollutants into waters of the United States in Idaho (except on tribal land) per IDAPA 58.01.25. IPDES permits are written to comply with state water quality standards and limit the amount of pollution that permitted facilities may discharge into surface waters.
Contact EPA Region 10 at (206) 553-1200 for projects on tribal lands. DEQ does not issue IPDES permits for facilities within tribal lands.
Quick Actions
Apply and Pay
- Contact your DEQ Regional Office to determine the appropriate permit type or discuss your project.
- Submit an application through IPDES E-Permitting.
- Apply for aquaculture or pesticide general permits via EPA Central Data Exchange.
- Pay any applicable fees through IPDES E-Permitting.
Submit Compliance Reports
Reports are due by the date specified in your permit.
- Submit Discharge Monitoring Reports (DMRs) via the EPA Central Data Exchange (CDX) — NeT-DMR system.
- Submit all other compliance reports through the IPDES E-Permitting System.
Report a Permit Violation
- Report public health emergencies immediately to (800) 632-8000.
- Give verbal notice to DEQ within 24 hours by calling (833) IPDES24 and your DEQ Regional Office.
- Submit a written report to DEQ via IPDES E-Permitting within five days.
Types of IPDES Permits
Individual IPDES Permits
An individual IPDES permit is issued to a specific facility or discharge and is tailored to the unique characteristics of that operation. Applicants must submit a comprehensive permit application. DEQ will conduct a full technical review before developing permit conditions specific to the discharge. Learn more about the different types of individual IPDES permits in the dropdowns below.
Municipal
Publicly Owned Treatment Works (POTWs) and Private Domestic Treatment Works (PDTWs) discharging to Idaho surface waters must hold an individual municipal IPDES permit. Permits are issued for five-year terms and must comply with IDAPA 58.01.02 and IDAPA 58.01.25.
Key Permit Conditions
- Compliance Schedules — If a reissued permit includes new or more stringent limits and immediate compliance is not feasible, the permit may include a compliance schedule.
- Effluent Limits — Common parameters include BOD₅, TSS, pH, E. coli, ammonia, and nutrients.
- Monitoring and Reporting — Collecting samples at required locations; testing using approved methods; submitting results electronically in regular reports.
- Pretreatment — Requirements are included directly in the permit. No separate pretreatment permit is issued in Idaho.
- Sludge and Biosolids — prepare and submit a Sludge Disposal Plan, also known as a Biosolids Management Plan
- Standard and Special Conditions — May include WET testing, thermal impact studies, and compliance schedules.
Apply
Guidance
Industrial
Individual industrial permits are issued to point-source dischargers that are not POTWs and are not appropriately covered by an IPDES general permit. Activities requiring industrial permit coverage for their discharge to surface waters include mining, silviculture, food processing, aquaculture, and concentrated animal feeding operations.
Apply
Guidance
General IPDES Permits
A general IPDES permit is issued by DEQ to cover multiple facilities or activities with similar discharge characteristics under one standardized set of requirements. Facilities seeking coverage typically submit a Notice of Intent (NOI) rather than a full permit application. Learn more about the different types of general IPDES permits in the dropdowns below.
Aquaculture — Concentrated Aquatic Animal Production (CAAP)
Fish processing and concentrated aquatic animal production (CAAP) facilities are defined in IDAPA 58.01.25.010 as a “hatchery, fish farm, or other facility which meets the criteria in Appendix C of 40 CFR Part 122, or which the Department designates under 40 CFR 122.24(c).”
Facilities eligible for coverage under these general permits must discharge pollutants to surface waters of the United States during at least 30 days per year. The facility must contain, grow, or hold fish in raceways, ponds, or other similar structures and meet at least one of the following criteria:
- For cold water aquatic species, the facility must produce 20,000 pounds or more of cold-water aquatic species per year and feed at least 5,000 pounds of food in any one calendar month.
- For warm water aquatic species, the facility must produce more than 100,000 pounds of warm water aquatic species per year.
Aquaculture Facilities Designated as CAAP on a Case-by-Case Basis under 40 CFR 122.24(c)
A facility not meeting the above requirements may still need to seek coverage if, after an on-site visit, DEQ determines the facility is a significant contributor of pollutants based on:
- Location and quality of the receiving water
- Holding, feeding, and production capacities of the facility
- Quantity and nature of the pollutants discharged
- Other relevant factors, such as TMDL determinations for the watershed
Apply
Submit a Notice of Intent (NOI) via the EPA Central Data Exchange (CDX)
Guidance
Permit Documents
Confined Animal Feeding Operations (CAFO)
A CAFO is a facility where animals have been, are, or will be stabled or confined and fed or maintained for a total of 45 days or more in any 12-month period and where vegetation is not sustained in the confinement area during the normal growing season.
Any CAFO that meets specific animal thresholds and discharges to a water of the US must obtain coverage under the CAFO general permit.
Coverage Thresholds for Concentrated Animal Feeding Operations:
| Animal | Minimum # for Coverage Requirement |
|---|---|
| Mature Dairy Cattle (milked or not) | 200 |
| Veal Calves | 300 |
| Cattle other than Mature Dairy Cattle | 300 |
| Swine weighing 55 lbs or more | 750 |
| Swine weighing less than 55 lbs | 3,000 |
| Horses | 150 |
| Sheep or Lambs | 3,000 |
| Turkeys | 16,500 |
| Laying Hens (with liquid manure handling) | 9,000 |
| Chickens (other than laying hens) | 37,500 |
| Laying Hens (with non-liquid manure handling) | 25,000 |
| Ducks (with non-liquid manure handling) | 10,000 |
| Ducks (with liquid manure handling) | 1,500 |
Permit Requirements
- Nutrient Management Plan (NMP) — Permitted CAFOs must develop and implement an NMP addressing manure and wastewater handling and storage, land application rates, site-specific nutrient management controls, and recordkeeping.
- Manure and Wastewater Storage Structures — Permitted CAFOs must prevent discharge except as allowed under the permit and agricultural stormwater provisions.
Coordination with Idaho State Department of Agriculture
The Idaho State Department of Agriculture (ISDA) regulates AFOs, CAFOs, and dairy farms pursuant to the Beef Cattle Environmental Control Act, the Dairy Environmental Control Act, the Poultry Memorandum of Understanding Environmental Act, and rules adopted under the authority of these Acts. DEQ and ISDA have a Memorandum of Understanding addressing how the two agencies coordinate permitting and inspecting CAFOs.
Apply
Submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
Drinking Water Treatment Facilities
The drinking water treatment facility general permit provides coverage for facilities that discharge treated wastewater from water treatment filtration processes (e.g., filter backwash, sedimentation/presedimentation wash-down, sedimentation/clarification, filter to waste) and their delivery systems to surface waters of the US.
Apply
Submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
Permit Documents
Groundwater Remediation
Owners and operators of facilities that pump and treat groundwater and discharge to waters of the US are eligible for coverage under the groundwater remediation general permit.
Operators of construction/excavation dewatering activities, building dewatering, and aquifer pump testing that occur at designated or known contaminated sites are also eligible for coverage.
Apply
Submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
Permit Documents
Pesticide General Permit (PGP)
The pesticide general permit (PGP) covers the application of biological or chemical pesticides that leave a residue. These pesticides may enter surface water when applied for mosquito and other flying insect pest control, weed and algae pest control, animal pest control, or forest canopy pest control use. Operators must seek coverage under the PGP under specified conditions.
Apply
Submit a Notice of Intent (NOI) via EPA Central Data Exchange (CDX) — NeT-PGP
Guidance
Permit Documents
Small Suction Dredge Mining General Permit (SSDMGP)
The small suction dredge mining general permit (SSDMGP) covers recreational suction dredging for waters open to mining, and it specifies limits on maximum nozzle size and cumulative horsepower rating.
Apply
Three permit authorizations are required before dredging:
- SSDMGP approval from DEQ
- Submit a Notice of Intent (NOI) through IPDES E-Permitting at least 60 days before you plan to start dredging
- Once received, post the permit certificate at the dredging site
- Idaho Department of Water Resources (IDWR) small-scale mining approval
- Federal land manager approval from one of the following:
- Bureau of Land Management (BLM) OR
- US Forest Service (USFS)*
Do not begin dredging until all three permit authorizations are received.
*Instructions for accessing the correct USFS contact: Select the State and the forest/grassland of interest and select “GO.” Then select the “Topics” tab and select “Geology.”
NOI Submittal Windows for Special Areas
NOIs must be submitted at least 60 days prior to dredging, however, special areas have specific timeframes for submittals.
| Special Area | NOI Window | Allocation Method |
|---|---|---|
| GEM Creeks | January 1 – April 1 each year | Allocated hours; number of permits limited |
| McCoy Creek | January 1 – May 1 each year | First come, first served; number of permits limited |
| Lolo Creek | January 1 – May 1 each year | First come, first served; number of permits limited |
| Moose Creek | January 1 – May 1 each year | First come, first served; number of permits limited |
| French & Orogrande Creeks | January 1 – May 1 each year | First come, first served; number of permits limited |
| South Fork Clearwater River (SFCW) | January 1 – March 1 each year | First 15 dredgers with all permits via interagency coordination |
Closed Waters
Any water closed by the permit, regardless of IDWR’s open/closed status, will not be granted coverage under general permit. The waters closed by the permit include:
- Nationally protected areas
- Tribal reservations
- National wild and scenic rivers
- Endangered species habitat areas
- Withdrawn river segments by Idaho Department of Lands
- State protected rivers
- Mercury or sediment-impaired streams without a waste load allocation for suction dredging
Nationally protected and designated critical habitat areas may be open under the general permit only if a federal agency has completed Endangered Species Act section 7 consultation.
Guidance
Permit Documents
DEQ Staff Contact
- For assistance completing your NOI, contact David Hotz at (208) 373-0178 or at David.Hotz@deq.idaho.gov, or make an appointment with your DEQ Regional Office to ensure appropriate staff are available to assist.
Stormwater — Construction General Permit (CGP)
Construction projects that disturb one or more acres and discharge stormwater must be permitted under the stormwater construction general permit.
Key Requirements
- Submit a Notice of Intent before earth disturbance begins
- Develop and maintain a Stormwater Pollution Prevention Plan (SWPPP) onsite
- Install and maintain best management practices (BMPs)
- Conduct regular inspections
Projects that disturb less than 5 acres and have a Rainfall Erosivity Factor (R factor) of less than 5 may qualify for a low erosivity waiver (LEW). Calculate R factor using the EPA Erosivity Calculator.
SWPPP Requirements
A SWPPP is required under the CGP (IDR100000) and MSGP (IDR050000). It must be completed before submitting a Notice of Intent.
What a SWPPP Must Include
- Identification of potential pollution sources
- Description of control measures (BMPs)
- Site map showing drainage and discharge points
- Inspection and maintenance procedures
- Corrective action procedures
Apply
Develop a SWPPP and then submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
- User’s Guide to Permitting and Compliance Volume 5: Stormwater
- Idaho BMP Catalog
- EPA CGP SWPPP Templates
Permit Documents
Stormwater — Multi-Sector General Permit (MSGP)
Industrial facilities exposed to stormwater must seek coverage under the multi-sector general permit (MSGP). Coverage is based on the facility’s standard industrial classification (SIC) code. Facilities required to obtain coverage based on their SIC code are listed in Appendix D of the MSGP Permit.
Facilities commonly covered in Idaho include mines, airports, and junkyards, as well as facilities that process food, cement products, wood products, and metal products.
Key Requirements
- Develop and maintain a Stormwater Pollution Prevention Plan (SWPPP) onsite
- Implement best management practices (BMPs) and conduct routine inspections
- Perform monitoring and submit required reports
Facilities that would otherwise require MSGP coverage based on their SIC code may qualify for a no exposure certification (NEC) if industrial activities and materials are not exposed to stormwater.
SWPPP Requirements
A SWPPP is required under the CGP (IDR100000) and MSGP (IDR050000). It must be completed before submitting a Notice of Intent.
What a SWPPP Must Include
- Identification of potential pollution sources
- Description of control measures (BMPs)
- Site map showing drainage and discharge points
- Inspection and maintenance procedures
- Corrective action procedures
Apply
- Develop a SWPPP and then submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
- User’s Guide to Permitting and Compliance Volume 5: Stormwater
- Idaho BMP Catalog
- EPA MSGP Fact Sheets and SWPPP Guidance
Permit Documents
Stormwater — Municipal Separate Storm Sewer Systems (MS4s)
Municipalities meeting certain population criteria must seek coverage under a separate municipal storm sewer system permit (MS4). MS4 permits cover public entities discharging stormwater, including cities, counties, the Idaho Transportation Department, state universities, local colleges, and local highway districts.
MS4s are regulated as large/medium (phase I) or small (phase II) systems.
- Phase I systems are defined as cities or certain counties with populations of 100,000 or more.
- Phase II systems are in Census-designated urban areas with population of 50,000 or more.
Urbanized areas owned by separate municipalities may be covered under one permit.
All permitted MS4s are required to implement six minimum control measures:
- Public education and outreach
- Public involvement
- Illicit discharge detection and elimination
- Construction site runoff control
- Post-construction stormwater management
- Municipal operations controls
Apply
Submit a Notice of Intent (NOI) via IPDES E-Permitting
Guidance
Apply or Renew
Individual Permits
How to apply:
- Contact your DEQ Regional Office to discuss your project (recommended).
- Submit an application through IPDES E-Permitting.
After you apply:
- DEQ reviews your application and may request additional information.
- The permit is added to the development queue on the Permit Issuance Plan.
- DEQ develops a draft permit when the permit is up for development in the queue.
- 10-day errors and omissions review.
- 30-day public comment period.
- Final permit issuance.
- 28-day appeal period.
Renew
- Renewal applications must be submitted through IPDES E-Permitting at least 180 days before the permit expires.
General Permits
How to apply:
- Contact your DEQ Regional Office to determine the appropriate permit type.
- Stormwater Construction General Permit (CGP) and Multi-Sector General Permit (MSGP): complete a Stormwater Pollution Prevention Plan (SWPPP) before submitting a Notice of Intent (NOI)
- Submit an NOI via IPDES E-Permitting.
- Aquaculture and Pesticide Permitting: Submit your NOI through EPA Central Data Exchange (CDX).
- Pay applicable fees. Coverage under a general permit is not authorized until all required fees have been paid.
After you apply:
- DEQ reviews the NOI and obtains external review if required.
- DEQ authorizes or denies coverage under the general permit.
Renew
- Reference the specific general permit language for renewal timeline information.
Note: Many Idaho IPDES permits are listed as “Admin. cont.” in the Permit Issuance Plan or on DEQ’s website, indicating the permit term is expired but the permit is still in effect because a timely renewal was filed. - To renew a general permit, submit an NOI via IPDES E-Permitting.
- Aquaculture and Pesticide Permitting: Submit your NOI through EPA Central Data Exchange (CDX).
Modify, Transfer, or Terminate a Permit
Permit Modifications
Modifications may be initiated by DEQ or by request of an interested person, including the permittee. Requests must be in writing and contain facts or reasons supporting the request.
- Minor permit modifications are administrative and do not require public notice.
- Major permit modifications require a 30-day public notice period.
Permit Transfers
- Submit a signed transfer agreement from both parties through the IPDES E-Permitting System at least 30 days before the propsed transfer.
- DEQ will review the transfer agreement and may issue a notice of intent to modify, or revoke and reissue the permit (a modification of a permit transfer is considered a minor modification.)
- If DEQ does not issue any notice, the transfer is effective on the date specified in the agreement.
Notices of Termination
Terminations may be initiated by DEQ or by request of an interested person, including the permittee. Permit terminations must meet the eligibility requirements in IDAPA 58.01.25.203.
- Submit a Notice of Termination (NOT) through the IPDES E-Permitting System.
- Aquaculture and pesticide general permit NOTs must be submitted through EPA Central Data Exchange (CDX).
- Permit coverage remains active until DEQ approves the NOT and notifies the permittee of the termination date.
Fees and Payments
IPDES fees are established under IDAPA 58.01.14.170. Annual fees are assessed October 1 and are due by December 30.
Fees vary based on permit type:
| Permit Type | Application Fee | Annual Fee |
|---|---|---|
| Individual Permits | ||
| Individual Permit Municipal | NA | $1.74 per EDU |
| Individual Permit Industrial — Major | $0 | $13,000 |
| Individual Permit Industrial — Minor | $0 | $4,000 |
| Construction General Permit (CGP) — IDR100000 | ||
| >0–10 acres | $200 | $0 |
| >10–50 acres | $400 | $75 |
| >50–100 acres | $750 | $100 |
| >100–500 acres | $1,000 | $400 |
| >500 acres | $1,250 | $400 |
| Low Erosivity Waiver | $125 | $0 |
| Multi-Sector General Permit (MSGP) — IDR050000 | ||
| Industrial MSGP | $1,500 | $1,000 |
| Certificate of No Exposure | $250 | $100 |
| Other General Permits | ||
| Other General Permits | $0 | $0 |
How to Pay
IMPORTANT: Notices of Intent (NOIs) will not be authorized until the applicable fee is paid. To avoid delays in processing of permits, DEQ strongly paying fees online. Mail in checks are allowed but may result in delayed permit application approval.
- Online (Preferred)
- Pay through IPDES E-Permitting
- By Mail
- Make checks payable to: DEQ
- Memo: invoice number
- Mail to:
Idaho DEQ Financial Office
1410 N. Hilton St.
Boise, ID 83706
Compliance Requirements
IPDES permits require permittees to conduct periodic evaluations of compliance with established effluent limits and report these to DEQ. IPDES permits specify what must be monitored, how often monitoring must occur, and how results must be reported.
- Permit-specific requirements are outlined in your issued IPDES permit.
- General compliance requirements are available in Section 9 of the IPDES User’s Guide to Permitting and Compliance Volume 1: General Information.
Submitting Reports
Reports are due by the dates specified in your permit. Submit reports using the appropriate system:
- Submit Discharge Monitoring Reports (DMRs) through EPA Central Data Exchange (CDX) — NeT-DMR .
- Submit all other compliance reports through the IPDES E-Permitting System.
Report a Permit Violation
- Report public health emergencies immediately by calling the 24-hour Idaho Emergency Medical Services Communications Center at (800) 632-8000.
- Give verbal notice to DEQ within 24 hours by calling (833) IPDES24 and your DEQ Regional Office.
- Submit a written report to DEQ via IPDES E-Permitting within five days.
Compliance Inspections
| Type | Description | Conducted By |
|---|---|---|
| Compliance Evaluation (CEI) | Full facility, records, outfall review | Regional or State IPDES Compliance Officer |
| Reconnaissance | Visual survey, no advance notice | Regional IPDES Compliance Officer |
| Performance Audit | In-depth treatment & sampling review | State Office IPDES Compliance Officer |
| Construction Site | Best Management Practice (BMP), Stormwater Pollution Prevention Plan (SWPPP) verification | Regional IPDES Compliance Officer |
| Follow-Up | Corrective action verification | Regional or State IPDES Compliance Officer |
Staff Contacts
IPDES E-Permitting Support
(833) IPDES24 / (833) 473-3724
IPDESe-permitting@deq.idaho.gov
Enforcement Questions
Main enforcement line: (208) 373-0182
wwenforcement@deq.idaho.gov
Individual Permits (Municipal & Industrial)
Matthew Stutzman
(208) 373-0247
Matthew.Stutzman@deq.idaho.gov
Stormwater Construction General Permit,
Drinking Water General Permit
Rebecca Garcia
(208) 373-0423
Rebecca.Garcia@deq.idaho.gov
Industrial Stormwater General Permit,
Small Suction Dredge Mining
David Hotz
(208) 373-0178
David.Hotz@deq.idaho.gov
Pretreatment,
Sewage Sludge and Biosolids
Vacant
(833) 473-3724
IPDESe-permitting@deq.idaho.gov
Aquaculture,
CAFOs,
Municipal Storm Sewer System (MS4),
Groundwater Remediation,
Pesticide General Permits
Patrick Gillis
(208) 373-0498
Patrick.Gillis@deq.idaho.gov
EPA Platforms (CDX, NeT-DMR, NeT-PGP, NeT-AQUA, ECHO, ICIS)
Brynn Lacabanne
(208) 373-0289
Brynn.Lacabanne@deq.idaho.gov
Other General Permit Questions
Angela Anderson
(208) 373-0560
Angela.Anderson@deq.idaho.gov