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New electronic fee payment option for Wastewater Construction permit applications and NPDES permits

  • 6/29/2023 3:16:00 PM
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The Wastewater Engineering and NPDES Sections now accept electronic payments for Wastewater Construction Permit applications and NPDES permit fees on the Iowa DNR Payment System.

Payment Information for Wastewater Construction and NPDES Fees:

  • Permittees and applicants can use the updated Iowa DNR Payment System effective July 1, 2023.
  • No separate invoice form will be needed for the electronic payments as the information will be entered online.
  • Payments can be made with a credit card or electronic check.
  • All payments will include a $1.50 processing fee.
  • Credit card payments will include an additional 2.5% processing fee.
  • The Payment System accepts Visa, MasterCard, Discover, and American Express.
  • Existing paper fee invoices do not need to be mailed separately when an electronic payment is made.

Wastewater Engineering Construction Permit Application Fees - Additional Information:

To pay a construction permit application fee, proceed to the Iowa DNR Payment System and choose “Pay Wastewater Construction Permit Fee” or use the direct link to the Wastewater Construction Fee Form webpage.

For more information or questions on construction permit application fees, please contact Rose Sanchez at (515) 725-8430 or, or Donna Gomm at (515) 725-8427 or

NPDES and Operation Permit Fees - Additional Information:

To pay an NPDES fee electronically (application, annual, or amendment), proceed to the Iowa DNR Payment System and choose “Pay Individual NPDES and Operation Wastewater Permit Fees,” or use the direct link to the Individual NPDES and Operation Wastewater Permit Fees webpage. Search for your fee using the permit number or facility name and follow the instructions on-screen.

The NPDES Section encourages using the Iowa DNR Payment System, but payments may continue to be mailed along with the NPDES fee invoice form or paid over the phone using a credit card.

Application Fees - The NPDES and Operation Permit application fee of $85 can now be paid using the Iowa DNR Payment System. Application fees are due when a permit application is submitted, usually once every five years. 

Annual Fees - The state fiscal year (FY) 2024 annual fees will be available in the Iowa DNR Payment System in mid-July. FY2024 payment notices and paper invoices will be mailed to each facility in July. Annual fee payments are due August 30 of each year and are not connected to permit renewals or the $85 application fee.

Amendment Fees - Until August 2024, do not pay amendment fees using the Iowa DNR Payment System. Due to a database error, the amendment fees in the Payment System are not all accurate at this time. The erroneous amendment fees will be removed in July. If you wish to pay an amendment fee using the Payment Portal before August 2024, contact the permit writer drafting the amendment before making a payment.

For more information or questions on the NPDES fees, please visit the NPDES Permit Fees webpage.