Polluted stormwater runoff from the City of McPherson is transported through the Municipal Separate Storm Sewer Systems (MS4s), from which it is discharged untreated into local waterbodies. This system includes gutters, inlets, pipes, ditches and culverts throughout the City. To prevent harmful pollutants from being washed or dumped into an MS4, the City must obtain a NPDES permit and develop a stormwater management program (SWP).

As authorized by the Clean Water Act, the National Pollutant Discharge Elimination System (NPDES) permit program controls water pollution by regulating point sources that discharge pollutants into waters of the United States. Industrial, municipal and other facilities must obtain permits if their discharges go directly to surface waters. The City of McPherson stormwater system discharges into Bull Creek, Turkey Creek and Mingenback Lake.