The National Pollutant Discharge Elimination System (NPDES) program is a State and Federal permitting program that regulates point sources that discharge pollutants to our waterways. For Municipal NPDES Programs, that point source is the storm drain system. Pollutants discharge to the storm drain system in stormwater and urban runoff. The purpose of the Municipal NPDES Program is to protect waterways by preventing and controlling polluted discharges to the storm drain system.