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NPDES Wastewater Permitting

General Information:

The NPDES Section of the Iowa Department of Natural Resources issues discharge permits under delegation of a federal program known as the National Pollutant Discharge Elimination System (NPDES) permit program. The NPDES program regulates the direct discharge of wastewater to surface waters. For more information on the Iowa DNR's NPDES Program, please see the discussion in the accordion below.

NPDES Email Contacts:

The NPDES Section accepts all mail electronically. Please submit all documents, except permit applications and fees, to

Individual NPDES and operation permit applications should be submitted via e-mail. Please see the individual NPDES application forms page for more information.

Electronic Permit Notifications:

Public notices and notifications for individual NPDES and operation permits are available electronically. Sign up for electronic notifications in the Wastewater Permit information Exchange (WWPIE) database. Sign up instructions are available in the WWPIE section of the NPDES Databases page.

NPDES Program

Iowa was delegated authority to administer the NPDES program by the EPA in 1978. Under Iowa's NPDES program, all facilities that discharge pollutants from any point source into waters of the United States or waters of the state are required to obtain an NPDES or operation permit, respectively. The permits require compliance with all federal and state standards and may require additional controls based on local conditions.

The term pollutant includes any type of industrial, municipal, and agricultural waste discharged into water. Pollutants can enter waters from a variety of pathways including agricultural, domestic, and industrial sources. These sources are categorized as either point sources or non-point sourcesPoint source discharges include those from publicly owned treatment works (POTWs), from industrial facilities, and from urban runoff.  While provisions of the NPDES Program do address certain types of agricultural activities, most agricultural facilities are defined as non-point sources and are exempt from NPDES regulation.

Pollutant contributions may come from both direct and indirect sources.  Direct sources discharge wastewater directly into a receiving waterbody, whereas indirect sources discharge wastewater to a POTW, which in turn discharges into a receiving waterbody.

Because POTWs are direct dischargers, they must obtain and comply with an NPDES permit.  If the concentration of pollutants leaving a POTW is too high, or if a POTW's discharges endanger public health or the environment, the facility violates its permit and can be fined and/or required to upgrade. A POTW may have trouble meeting its NPDES permit conditions if the amounts of pollutants in the wastewater flowing into the treatment plant (influent wastewater) are too high. One way to reduce pollutants in influent wastewater is to require pretreatment. Thus, the conditions of a POTW's permit might dictate the need for pretreatment.

Industries that are direct dischargers to surface waters must also obtain and comply with an NPDES permit. Industries who discharge wastewater to a municipal sewer system may be required to have a treatment agreement. The NPDES Section reviews treatment agreements for conformance to federal and state pretreatment requirements. Some larger cities have accepted responsibility for administering local pretreatment programs that regulate industrial discharges in their community.

To read more about wastewater, please view the following article from the Iowa Conservationist: Down the Drain: What Happens to Our Wastewater?  (*.pdf file)

An NPDES permit is a license for a facility to discharge a specified amount of pollutants into a receiving water under certain conditions.  The permit limits the amount of pollutants a wastewater treatment plant may discharge.  The two basic types of NPDES permits are individual and general permits. 

An individual permit is a permit specifically tailored to an individual facility.  Once a facility submits the appropriate permit application(s), the Iowa DNR develops a specific permit based on the information in the application and issues the permit to the facility for a specific time period (usually five years) with a requirement that the facility reapply prior to the expiration date.

A general permit covers multiple facilities within a specific category.  General permits are a cost-effective option because a large number of facilities that can be covered under a single permit.  General permits may be written to cover categories of point sources having common elements, such as:

  • Facilities that involve the same or substantially similar types of operations;
  • Facilities that discharge the same types of wastes;
  • Facilities that require the same effluent limits or operating conditions; and
  • Facilities that require the same or similar monitoring.

By issuing general permits, the Iowa DNR can allocate resources in a more efficient manner to provide more timely permit coverage.  For example, a large number of facilities that have certain elements in common may be covered under a general permit without expending the time and money necessary to issue an individual permit to each of these facilities.  In addition, using a general permit ensures consistency of permit conditions for similar facilities.  For more information on Iowa’s general NPDES permits, see the NPDES General Permits page.

All NPDES permits, at a minimum, consist of five general sections:

  1. Cover Page - Typically contains the name and location of the permittee, a statement authorizing the discharge, and the specific locations for which a discharge is authorized.
  2. Effluent Limits - The primary mechanism for controlling discharges of pollutants to receiving waters. Permit writers spend a majority of their time deriving appropriate effluent limits based on applicable technology-based and water quality-based standards.
  3. Monitoring and Reporting Requirements - Used to characterize waste streams and receiving waters, evaluate wastewater treatment efficiency, and determine compliance with permit conditions.
  4. Special Conditions - Conditions developed to supplement effluent limits. Examples include: best management practices (BMPs) and additional monitoring.
  5. Standard Conditions - Preestablished conditions that apply to all NPDES permits and delineate the legal, administrative, and procedural requirements of the permit.

The NPDES permitting process begins when the owner of the facility (permittee) submits an application. After receiving the application and making a decision to proceed with the permit, a permit writer reviews the application for completeness and accuracy. When the application is complete, a permit writer develops a draft permit and the justification for the permit conditions (referred to as the permit rationale).

The first major step in the permit development process is deriving technology-based effluent limits based on federal standards. Following this step, a permit writer derives effluent limits that are protective of state water quality standards (i.e., water quality-based effluent limits). A permit writer then compares the technology-based and water quality-based effluent limits and applies the more stringent limits in the permit. The decision-making process for deriving limits is documented in the permit rationale. A permit may have limits that are technology-based for some parameters and water quality-based for others.

Following the development of effluent limits, a permit writer develops appropriate monitoring and reporting conditions, facility-specific special conditions, and includes standard conditions that are the same for all permits. After the draft permit is complete, the Iowa DNR provides an opportunity for public participation in the permit process. A public notice announces the permit and interested parties may submit comments regarding the draft permit. The public can sign up for email notifications of new draft permits on the Wastewater Permit Information Exchange (WWPIE) system.  Based on the comments, a permit writer then develops a final permit, documents the decisions for the administrative record, and issues the final permit to the facility. All final NPDES and operation permits can be viewed on the WWPIE system.

Hot Topics

EO10 Rulemaking:

Executive Order 10 (EO10), signed by the Governor in January of 2023, requires all state agencies to identify which administrative rule chapters will be retained or rescinded. For more information on proposed EO10 changes to the wastewater rules, please see the Water Quality Rulemaking page.

Electronic Fee Payments:

The NPDES Section now accepts electronic payments for individual NPDES annual, application and amendment fees. To make an electronic payment, proceed to DNR Payment Portal 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. For more information on the fees, please see the NPDES Fees page.

Renewal of NPDES General Permits:

In 2022, General Permits 5 (mining), 6 (wells), 7 (pesticides), 8 (hydrostatic), and 9 (dewatering) were renewed effective July 1, 2023. The storm water general permits (GPs 1-3) and the onsite wastewater general permit (GP 4) were renewed effective March 1, 2023. For more information on these general permits, please see the NPDES General Permits page.

Disadvantaged Communities:

For more information on how a community or entity can qualify as disadvantaged, please see the Rural Community Sewers page.