The Nebraska Department of Environment and Energy (NDEE) regulates Municipal Separate Storm Sewer Systems (MS4s) under the National Pollutant Elimination Discharge System (NPDES) Program. The purpose of NDEE’s MS4 Program is to reduce or prevent pollutants from entering a waterbody by way of stormwater runoff. 

MS4s are the collection systems owned by a state, city, town, village or other public entity that are used to collect or convey stormwater (e.g., storm drains, pipes, or ditches). MS4s only handle stormwater and are not a combined sewer, a sanitary sewer, or publicly owned treatment works.

As MS4s discharge untreated stormwater into local water bodies, NDEE is responsible for permitting MS4s to manage pollutants such as sediments and bacteria. NDEE regulates MS4 permittees and works with them to prevent pollution in stormwater.

The public entity, or operator, is identified by NDEE as requiring a permit. In Nebraska, this includes municipalities of 100,000 people or more as large or medium MS4s (Lincoln and Omaha respectively) and small MS4s of 10,000 people or more.

Small MS4s may also include other public groups that need to dispose of stormwater. These include smaller municipalities, urban areas of counties, and non-traditional MS4s such as the Nebraska Department of Transportation, University of Nebraska, and Offutt Air Force Base. 

There are currently 26 permitted MS4s in the state of Nebraska. Permits are valid for five years. As part of the MS4 permitting process, municipalities applying for a municipal stormwater permit must submit a stormwater management plan (SWMP) to the Department. This SWMP contains practices that will reduce stormwater pollutants and protect Nebraska waterbodies. 

A stormwater management plan requires an MS4 permittee to educate and inform the public about stormwater, inspect and manage construction sites, investigate illegal discharges (spills, dumping, complaints), manage stormwater for permanent sites, and also manage stormwater for publicly owned buildings such as maintenance yards. 

The Department inspects MS4s every five years. The inspection is based on the practices in the SWMP. Permitted municipalities are also required to submit an annual report to NDEE. The agency does not review design standards for storm sewers as it is a local engineering requirement. NDEE does inspect stormwater complaints, construction sites, industries, and will work notify MS4s if there are complaints in their area.

Stormwater was added to the NPDES program following the Nationwide Urban Runoff Program research project conducted from 1979 to 1983 by the United States Environmental Protection Agency (EPA). This first comprehensive study of urban stormwater pollution found that urban development is a significant contributor to pollutants discharged in stormwater. Much of this is caused by development increasing the volume and intensity of stormwater discharges and the increased exposure of pollutants to precipitation.