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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-storm water 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-storm water 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 storm water only permit. 

Each facility subject to an individual non-storm water 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 storm water only permit and a non-storm water NPDES permit must submit separate payments.

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 signed fee invoice.  Checks not accompanied by an invoice will be returned.  If you wish to pay an annual or application fee by credit card, please fax your completed fee invoice to 515-725-8202, and call 515-725-8200 fifteen minutes after faxing in your invoice. 


Annual Fees for Individual NPDES permits:

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

Permit/ Facility Type
Annual Fee Amount
Major Municipal Facility (>1 MGD, AWW design flow) One thousand two hundred seventy-five ($1,275) 
Minor Municipal Facility (<1 MGD, AWW design flow) Two hundred ten ($210) 
Semi-public Facility (facility not owned by a city, sanitary sewer district, or management agency) Three hundred forty ($340)
Operation Permit (no wastewater discharge to Waters of the US) One hundred seventy ($170)
Major Industrial Facility (designated by EPA as a major) Three thousand four hundred ($3,400)
Minor Industrial Facility (not designated as a major) Three hundred ($300)
Open Feedlot Operation (AFO NPDES permit) Three hundred forty ($340)
Municipal Water Treatment Facility A fee shall not be charged ($0)

Annual fees are due by August 30 of each yearThe Department mails annual invoices each July that specify the annual fee due from each facility.

For a new facility that has not previously been issued an individual non-storm water NPDES permit or an operation permit, a prorated amount will be due 30 days after the 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, and the prorated amount will be due 30 days after the new permit is issued.

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

Failure to submit the appropriate annual fee may result in revocation or suspension of the facility's NPDES or operation permit.


Permit Application Fees for Individual NPDES and Operation permits:

For all non-storm water only NPDES permits and operation permits, a single application fee of $85 is due at the time of application.  The application fee is to be submitted with the application forms at the time of a new application or renewal 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 required $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-storm water 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 amendment fee of $85 is due.  If an amendment request is denied, the facility will be notified and no amendment fee will be required.

Because the amendment fee requirement is contingent upon the approval of the amendment request, permittees should submit amendment requests without the $85 application fee.  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.


Fees for Individual & General NPDES Storm Water Permits (General Permits 1, 2, & 3):

For individual storm water only permits, a one-time, multiple-year fee of $1,250 must be submitted at the time of application.  A storm water only permit is an NPDES permit authorizing the discharge of only storm water and any allowable non-storm water as defined in the permit.  Additional fees for individual storm water permits and for General Permits 1, 2, and 3 are specified in Chapter 64 of the Iowa Administrative Code.  An applicant can either pay an annual permit fee or a multiyear permit fee when the Notice of Intent for Coverage is submitted.  For more information about individual and general permits for storm water only discharges and their fees, please refer to the NPDES Storm Water Permit Application Options and Fees page.


Fees for Non Storm Water NPDES General Permits (4, 5, 6, & 7):

NPDES General Permit #4 - Discharge from Onsite Wastewater Treatment and Disposal Systems, no fees are required.

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 the Notice of Intent for Coverage is submitted.

NPDES General Permit #6 - Well Construction and Well Service Discharges, no fees are required.

NPDES General Permit #7 - Pesticide Discharges, no fees are required.


Wastewater Construction Permit Fees:

An application fee of $100 must be submitted with an application for any type of construction permit.  A 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, please refer to Wastewater Construction webpage.


Questions on NPDES Permit Fees:

For more information on any of the fees or for questions on fee payment, please contact Courtney Cswercko at 515-725-8411 or courtney.cswercko@dnr.iowa.gov.


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