Because Winder is divided by a substantial ridgeline, the City is served by two sewage treatment facilities: the Cedar Creek facility, serving the area north of the Seabord Railroad Line, and the Marburg Creek facility, serving the area south of this line. The Cedar Creek facility was updated in 1988 from a 500,000 gallon per day (gpd) secondary treatment facility to a 1.65 million gpd spray irrigation (land application) facility. The spray fields are scheduled for renovation (i.e. vegetation replacement) in 2003 and 2004. An upgrade of the Marburg Creek facility, consisting of land identification and acquisition, planning, design, regulatory approval and construction, began in 1997 and was completed in 2000. The capacity of the Marburg Creek plant was increased from 600,000 gpd to 1.5 million gpd. The effluent from the upgraded plant can be discharged into the stream, sprayed on city-owned dedicated spray fields, or used to provide irrigation water for non-agricultural uses. Currently, the Chimneys Golf Course and the Barrow County Recreation Department are using this reuse water for this purpose. The Marburg Creek treatment facility is one of the few totally enclosed sewage treatment plants in the state. Unlike the City of Winder's Water System, which serves both the City and a large portion of Barrow County, the sewer system is confined to the city limits of Winder, except for key industrial areas outside of the City.

The system currently supports approximately 3700 connections, and has a system of some 75 miles of sewer main.