The Town of Stonington's Water Pollution Control Authority office is located inside Town Hall at 152 Elm Street in Stonington. The Water Pollution Control Authority maintains the sewer systems throughout town. There are three separate sewer systems that serve parts of Stonington. Harold W. Storrs is the director of the Water Pollution Authority.
The Solid Waste and Recycling Office is located in Stonington's town hall along with many of the town's other offices and departments. The transfer station is located on Greenhaven Road. The Solid Waste & Recycling Office oversees the town's mandatory recycling program, waste program and provides information on hazardous waste and what can and cannot be recycled.