IDOT ensures that highway construction projects and highway separate storm sewer systems in urbanized areas comply with the National Pollutant Discharge Elimination System (NPDES). This is a permitting program, under the Federal Clean Water Act, which regulates construction, industrial activities and both large and small metropolitan separate storm sewer systems to reduce the discharge of pollutants into waters of the United States. Whenever an acre or more of ground is disturbed for roadwork, it is IDOT's responsibility to implement measures to control the discharge of sediment and other pollutants into nearby rivers, streams and wetlands. This is done through the use of an Erosion and Sediment Control Plan, which implements a variety of temporary and permanent measures (e.g. perimeter silt fence, ditch checks, temporary and permanent seeding) to prevent soil and other pollutants from leaving the construction site.

IDOT teaches classes concerning erosion and sediment control to local agencies, consultants, contractors, and its own personnel. The department has an Adopt-A-Highway Program that allows local community groups to pick up litter from our highways. All IDOT staff responsible for the application of herbicides are trained and licensed by the Illinois Department of Agriculture (IDOA), and all chemicals are stored in compliance with the IDOA's regulations.