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NPDES Permit Fees

Fees for NPDES permits, wastewater operation permits, and wastewater construction permits are established in section 455B.197 of the Code of Iowa. The NPDES fees and an explanation of the payment requirements are discussed below.

For individual non-stormwater NPDES permits and operation permits, a permittee must submit an application fee when applying for a permit, the appropriate annual fee each year, and an amendment fee when a request for a permit amendment is granted. A non-stormwater NPDES permit is defined as any individual NPDES permit or operation permit issued to a municipality, industry, semi-public facility, or animal feeding operation that is not an individual stormwater only permit. Each facility subject to an individual non-stormwater NPDES permit must pay an annual fee based on facility type. If a facility is covered under more than one NPDES permit, fees for each permit must be submitted individually. Facilities needing coverage under both a stormwater only permit and a non-stormwater NPDES permit must submit separate payments.

Payment Options:

Electronic - The NPDES Section now accepts electronic payments for individual NPDES annual, application and amendment fees. To make an electronic payment, proceed to and choose “Pay Individual NPDES and Operation Wastewater Permit Fees”. Search for your fee using the permit number or facility name and follow the on screen instructions. Payments can be made with credit card or electronic check. All payments will include a $1.50 processing fee, and credit card payments will include an additional 2.5% processing fee.

Credit Card over the Phone - If you wish to pay by credit card, email your completed fee invoice to, and call 515-725-8200 to make a payment.

Paper - Fees can be paid by check or money order made payable to the "Iowa Department of Natural Resources". All checks must be accompanied by a completed fee invoice. Checks not accompanied by an invoice will be returned.

Annual Fees for Individual NPDES and Operation permits:

For coverage under an individual non-stormwater NPDES permit, the following annual fees apply:

Permit/ Facility Type Annual Fee Amount
Major Municipal Facility (>1 MGD, AWW design flow) $1,275
Minor Municipal Facility (<1 MGD, AWW design flow) $210
Semipublic Facility (facility not owned by a city, sewer district, etc.) $340
Operation Permit (no wastewater discharge to Waters of the US) $170
Major Industrial Facility (designated by EPA as a major) $3,400
Minor Industrial Facility (not designated as a major) $300
Open Feedlot Operation (AFO NPDES permit) $340
Municipal Water Treatment Facility $0 (none)

Annual fees are due by August 30 of each year. The Department mails annual invoices each July that specify the annual fee due from each facility. Failure to submit the appropriate annual fee may result in revocation or suspension of the facility's NPDES or operation permit.

For a new facility that has not previously been issued an individual permit, a prorated amount will be due 30 days after a new permit is issued. The prorated amount is calculated by multiplying the annual fee by the number of months remaining in the state fiscal year divided by twelve. Each new facility will be sent an Annual Fee Invoice that specifies the amount due when their permit is issued.

Annual Fee Invoice (no fee amount specified) DNR Form #542-1254

Permit Application Fees for Individual NPDES and Operation permits:

For all non-stormwater only NPDES permits and operation permits, a single application fee of $85 is due at the time of application. Only one fee is required per application; e.g. submittal of Industrial Forms 1, 2, and 5 will require only one fee.
Application Fee Invoice (renewal application)  DNR Form #542-1251

A New Discharger is a facility that does not have a current NPDES permit. When a facility applies for an NPDES permit for the first time, the Application Fee Invoice for a New Discharger should be used. The $85 application fee for a New Discharger is the same as that for a renewal application.
Application Fee Invoice for a New Discharger  DNR Form #542-1253

Failure to submit the $85 fee at the time of application for a non-stormwater NPDES or operation permit renders the application incomplete. A permit application is not processed until the fee is received.

Amendment Fees for Individual NPDES and Operation permits:

When an amendment request is submitted, it will be reviewed to determine if the proposed amendment is reasonable and feasible. If the NPDES section determines that the permit can be amended, the facility will be notified that the amendment request was approved and that the $85 fee is due. If an amendment request is denied, the facility will be notified and no amendment fee will be needed.

Because the amendment fee is contingent upon the approval of an amendment request, permittees should NOT submit the amendment fee with an amendment request.. If a fee is submitted with an amendment request and the amendment is subsequently denied, the fee cannot be returned.

Before the NPDES Section can amend a permit based on an approved amendment request, the amendment fee must be submitted. If the required fee is not submitted, the permit in question will not be amended. Amendment fees will not be charged when an amendment request is submitted by DNR staff, when the request is to correct an error in the permit, or when the request is to change only the owner or facility name or address.

NPDES Stormwater Permit Fees; Individual and General (1, 2, & 3):

A stormwater only permit is an NPDES permit authorizing the discharge of only stormwater and any allowable non-stormwater as defined in the permit.

All stormwater general permit Notices of Intent (applications) must be accompanied by one of the following fees:
1 year - $175.00    3 years - $350.00    4 years - $525.00    5 years - $700.00

For individual stormwater only permits, a one-time, multiple-year fee of $1,250 must be submitted at the time of application.

For more information about general and individual NPDES permits for stormwater only discharges and their fees, please refer to the NPDES Stormwater Permit Application Options and Fees page.

Other NPDES General Permit Fees (4, 5, 6, 7, 8 & 9):

NPDES General Permit #5 - Mining and Processing Facilities, refer to the General Permit #5 webpage. An applicant can either pay an annual permit fee or a multiyear permit fee when a Notice of Intent is submitted.

No fees are required for the following General Permits: 

  • General Permit #4 - Discharge from Onsite Wastewater Treatment and Disposal Systems
  • General Permit #6 - Well Construction and Well Service Discharges
  • General Permit #7 - Pesticide Discharges
  • General Permit #8 - Discharge from Hydrostatic Testing, Tank Ballasting and Water Lines
  • General Permit #9 - Dewatering and Residential Geothermal Systems

Wastewater Construction Permit Application Fees:

An application fee of $100 must be submitted with an application for any type of wastewater construction permit. A wastewater construction permit is written approval from the DNR to construct a wastewater disposal system or part thereof in accordance with the approved plans and specifications. Construction, installation or modification of any wastewater disposal system, including sanitary sewer extensions, requires a construction permit issued by the DNR. For more information and the fee form, refer to the Wastewater Construction Permits webpage.

The Wastewater Engineering Section accepts electronic payments for wastewater construction permits. To make an electronic payment, proceed to, choose “Pay Wastewater Construction Permit Fee” and follow the online instructions.

Questions on NPDES Permit Fees:

For more information on any of the fees or for questions on fee payment, please contact Courtney Cswercko at