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National Pollutant Discharge Elimination System (NPDES) Program

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). The Iowa Department of Natural Resources was delegated NPDES authority 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 Iowa DNR issues three types of General NPDES Permits related to stormwater management.

  1. General Permit No. 1 (GP#1), Storm Water Discharge Associated with Industrial Activity
  2. General Permit No. 2 (GP#2), Storm Water Discharge Associated with Construction Activity
  3. General Permit No. 3 (GP#3), Storm Water Discharge Associated with Asphalt Plants, Concrete Batch Plants, Rock Crushing Plants, Construction Sand, Gravel Facilities

The IDNR has also issued individual stormwater permits to cities and universities under their MS-4 (Municipal Separate Storm Sewer System) program. Cities and universities are selected based on population, proximity to an urban area and/or discharge to an impaired waterbody. You will be contacted by the Iowa DNR if a MS-4 permit is required by your community. In all permits a Stormwater Pollution Prevention Plan is required.


Local Permits

Cities and counties throughout Iowa may issue permits related to stormwater activities for grading, construction site erosion and sediment control, post construction stormwater and floodplain management. Contact your local city or county for details on a local level. Relevant ordinances can be found in a city's code of ordinance, or may be listed on the Communities tab of this website.


Wetland Permits

In addition to a General Permit, construction, excavation or filling in streams, lakes, wetlands, or flood plains may require a Section 401 permit from either or both the Army Corps of Engineers and Iowa DNR. A Joint Application Form (Protecting Iowa Waters) shall be submitted to both agencies to begin the permit process for any of the following activities:

  1. Cutting the bank of a river, stream, or lake;
  2. Any excavation or dredging in a wetland, lake, stream or river;
  3. Channel changes or relocations (including stream straightening);
  4. Construction of any permanent dock, pier, wharf, seawall, boat ramp, beach, intake or outfall structure on a stream, river or lake;
  5. Placement of any fill, riprap, or similar material in a stream, river, lake, or wetland;
  6. Construction of a dam across any waterway;
  7. Placement of fill, construction of levees, roadways and bridges and similar activities on a floodplain, or construction of buildings on a flood plain; or
  8. Any construction on, above, or under all fee title lands and waters, dedicated lands and waters under the jurisdiction of the Natural Resource Commission (Commission) and managed by the Commission for public access to a meandered sovereign lake or meandered sovereign river; meandered sovereign lakes; meandered sovereign rivers; and sovereign islands (except those portions of the Iowa River and Mississippi River where title has been conveyed to Charter Cities).