A stormwater sewer is not treated; it goes directly to water body, pollutants and all.  A sanitary sewer goes to the waste water treatment plant where the water goes through a complicated process where it is cleaned and released back into the water. 

Stormwater sewers go directly to local water bodies without being treated. Sanitary sewers go to a wastewater treatment plant to be treated before discharging into a local water body.