Water Protection Program fact sheet
Division of Environmental Quality Director: Art Goodin
PUB2456

What is the fee for each application?

The Missouri Department of Natural Resources is required by law to review fee amounts periodically, which may change the fee amounts. Based on revisions to Code of State Regulations 10 CSR 20-6.011, effective Jan. 1, 2015, permit fees changed pursuant to Missouri Revised Statutes section 644.054, RSMo and section 644.057, RSMo. The Clean Water Fee helps pay for much of the work necessary to run the National Pollutant Discharge Elimination System (NPDES) permitting program; however, there are critical gaps that need to be filled to keep an effective program with state delegation.

Land Disturbance Permit Application Fee

The ePermitting system is being developed in phases, so not all of the permit types and permit categories will be available when ePermitting is implemented. Phase 1 went online in June 2012 and covered Land Disturbance Permits (MORA00000). Future phases will contain other general permits, construction permits (sewer extensions), Permits-by-Rule and individual general permit covered facilities needing to be public noticed.

Application for Termination Only Fee

No application fee is required for terminating a permit. However, it may be in the permittee's best interest to have all fees paid in full before submitting an application for termination. Failure to pay annual fees is a violation of the Missouri Clean Water Law and its implementing regulations. Outstanding annual permit fees may cause the termination application to be revoked.

What are the accepted payment types?

When making a payment in the ePermitting system, the user actually will make the payment through a private, third-party site known as Collection Services Inc., or CSI. The payment types accepted are credit card, debit card and electronic checks (e-checks).

What do I do if I don’t have a credit card or electronic check?

If the user does not have a credit card, debit card or e-check, the user cannot use ePermitting. The user will need to contact the department’s Central Office and request permission to submit a paper application.

Which credit card companies are accepted?

  • Visa®
  • Master Card® 
  • Discover®

Why can’t state agencies use ePermitting?

The State of Missouri Purchasing Card Policy and Procedure Manual, revised August 2022, was drafted and finalized by the Missouri Office of Administration. Chapter 7, section 7.5 Interagency Payments states, “Payments to other State Agencies are not allowed on the P-card. Examples include, but are not limited to, payments to MVE [Missouri Vocational Enterprises], Secretary of State (SOS), Missouri State Highway Patrol, State Printing, MO Revisor of Statutes, Department of Natural Resources, Division of Professional Registration, etc. Payments for goods or services to State Agencies should be processed directly through the State’s financial system."

This means other state agencies and the Department of Natural Resources cannot use ePermitting to receive an issued permit.

What happens to my application if my payment is not successfully processed?

When the user enters all applicable information in the CSI portion in the ePermitting system, there is chance the payment may not be successfully processed. The CSI system will generate several different messages for a whole host of problems that could have occurred. The message CSI generates should provide some detail of the problem. Regardless of the type of error, if the payment is not processed, the permit application cannot be finalized/ issued. The user should make sure all information entered is correct and the form of payment is acceptable in the ePermitting system.

What happens to my application if my payment is successfully processed?

When the payment is successfully processed by CSI, the ePermitting Confirmation Screen will appear. From this screen, the user will access the ePermitting home page to receive their issued operating permit.


Nothing in this document may be used to implement any enforcement action or levy any penalty unless promulgated by rule under chapter 536 or authorized by statute.


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