The City owns and operates a waste water collection and treatment facility.  The City's waste water treatment facility (WWTF) is located on the south side of the City and discharges treated waste water to the Mississippi River.  Wastewater generated through the facility's service area is conveyed to the treatment facility through gravity sewer and four watewater lift stations.

St Croix Bluffs Lift Station North Pearl Installed 2004
Dairy Queen Lift Station Hwy 10 Installed 1990
Main Lift Station 2nd Street Upgraded 1994
South Lift Station Hwy 35 South Installed 1988

The original WWTF was constructed in 1970 and consisted of an extended aeration activated sludge package plant with chlorination and discharge to the Mississippi River.  The WWTF was upgraded in 1995 to include preliminary treatment, biological (and chemical) phosphorous removal, addition of a second package plant, sludge thickening and thickened sludge storage, and UV disinfection.  The City of Prescott is one of 11 member owners of the West Central Wisconsin Biosolids Facility located in Ellsworth WI.  Waste sludge from the City's WWTF is sent to the Biosolids Facility for dewatering.  Centrate water is received back from the Biosolids Facility and discharged into the septage receiving station and mixed with the influent waste water from the City.

As of May 2010, the existing wastewater treatment facility was at approximately 72% of its design capacity.  Since it typically takes several years between the initiation of planning and the start-up of new wastewater facilities, the City decided to begin the planning process in 2010.   The City hired MSA Professional Services to evaluate alternatives for meeting the City's existing and future wastewater treatment needs.  As the existing WWTF has limited space for expansion, the alternatives evaluated included upgrading the existing facilities, regional treatment, and building a new WWTF at a new site.  Based on future flows, loads, evaluation of the current system, effluent limits, evaluation of alternative sites, and cost, the City Council approved upgrading the existing package plant and adding a new aerobic digester on site.  Upgrading the system will be dependent on the capacity of the current plant and is anticipated to start in 2014 or later.