NPDES Wastewater Permitting

The NPDES Section of the Iowa Department of Natural Resources issues discharge permits under delegation of a federal program known as the NPDES (National Pollutant Discharge Elimination System) permit program.  The NPDES program regulates the direct discharge of wastewater to surface waters.  The authority to issue NPDES permits rests either with a state or with the U.S. Environmental Protection Agency (EPA).  For more information on the NPDES Program in Iowa, please use the links below:

Hot Topics

Renewal of General Permit #5: NPDES General Permit #5 for Mining and Processing Facilities was reissued on July 20, 2016, All facilities who wish to continue their coverage under GP5 must submit a Notice of Intent for Coverage no later than January 15, 2017, using the NOI form on the GP5 webpage.

Proposed General Permits for Hydrostatic Testing and Dewatering: The NPDES Section is in the process of developing two new general permits. Proposed General Permit #8 will be for Hydrostatic Testing, Tank Ballasting, and Water Lines. Proposed General Permit #9 will be for Dewatering Activities and Residential Geothermal Discharges. For more information and drafts of the general permits, please refer to the NPDES General Permit #8 and the NPDES General Permit #9 webpages.

Nutrient Strategy: The Iowa Nutrient Reduction Strategy is a science and technology-based approach to assess and reduce nutrients delivered to Iowa waterways and the Gulf of Mexico. It outlines voluntary efforts to reduce nutrients in surface water from both point sources, such as wastewater treatment plants and industrial facilities, and nonpoint sources, including farm fields and urban areas, in a scientific, reasonable and cost effective manner. The full strategy is available at  For more information on the effects of the Nutrient Reduction Strategy on wastewater treatment plants, please refer to the Nutrient Strategy wastewater fact sheet.

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

NPDES Program Basics

States gain approval to administer the NPDES program by demonstrating their program meets federal requirements.  Iowa was delegated NPDES authority by EPA in 1978.

Under Iowa's NPDES program, all facilities that discharge pollutants from any point source into surface waters are required to obtain an NPDES or operation permit from IDNR. The permits require compliance with all federal standards, state rules, and state administrative code.

The term pollutant includes any type of industrial, municipal, and agricultural waste discharged into water. Pollutants can enter waters by many pathways including agricultural, domestic, and industrial sources.  These sources are generally categorized as either point sources or non-point sources.

Typical point source discharges include discharges from publicly owned treatment works (POTWs), discharges from industrial facilities, and discharges of urban runoff. While provisions of the NPDES Program do address certain 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 point sources.  Direct point sources discharge wastewater directly into a waterbody, whereas indirect point sources discharge wastewater to a POTW, which in turn discharges directly to surface waters.

Because POTWs are direct dischargers, they must obtain an NPDES permit. If the amount of pollutants leaving a POTW is too high, or the discharge endangers public health or the environment, the facility may violate its permit and can be fined or required to upgrade. A POTW may have trouble meeting its NPDES permit conditions if there are too many pollutants in the wastewater flowing into the treatment plant. One way to reduce pollutants in influent wastewater is to require industrial pretreatment, and a POTW's permit might dictate the need for pretreatment. Some larger cities in Iowa have accepted responsibility for administering local pretreatment programs that regulate industrial discharges in their city.

Industries, businesses, and other privately-owned facilities that discharge directly to surface waters must also obtain an NPDES permit. Industries who discharge wastewater to a POTW may be required to have a treatment agreement with the POTW. The NPDES Section reviews treatment agreements for conformance to federal and state pretreatment requirements.

To read more about wastewater, please view the following article from the Iowa Conservationist: Down the Drain: What Happens to Our Wastewater?

Types of NPDES Permits

An NPDES permit is a license for a facility to discharge a specified amount of a pollutants into a waterbody 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 an application, a permit writer develops a permit based on the application and issues the permit for a specific time period (generally 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 cost-effective because many facilities can be covered under a single permit. General permits can be written to cover categories of point sources having common elements. By issuing general permits, DNR can allocate resources more efficiently and can provide more timely permit coverage.  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.

Major Components of an NPDES Permit

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 limit guidelines.  Examples include: best management practices (BMPs) and additional monitoring activities.
  5. Standard Conditions - Pre-established conditions that apply to all NPDES permits and delineate the legal, administrative, and procedural requirements of the permit.

Development of an Individual NPDES Permit

The NPDES permitting process begins when the owner of a facility submits an application.  A permit writer in the NPDES section will review the application and contact the applicant if needed.  When the application is complete, a permit writer develops a draft permit and justification for the permit conditions (referred to as the permit rationale).

To develop a permit, a permit writer will first derive technology-based effluent limits (often from federal regulations). Next, the permit writer will derive effluent limits to protect state water quality standards (water quality-based effluent limits). Then, the technology and water quality-based effluent limits are compared, and the more stringent limits are applied in the permit. The decision-making process for deriving limits is documented in the permit rationale. A permit may have both technology-based and water quality-based effluent limits.

After effluent limits are developed, the permit writer will set monitoring and reporting conditions, set facility-specific special conditions, and include the standard permit conditions. Once a draft permit is complete, the public can submit comments regarding the permit. A public notice will announce a draft permit, the due date for comments, and the means for submitting comments.  After the comment period, the permit writer will develop a final permit, respond to any comments, document any final decisions, and issue a final permit.

For more information about Iowa's NPDES permits and permit program, please use the links in the left navigation bar.