Early phases of the project included rehabilitation of the facilities influent pumping station, new primary clarifiers, replacing RBCs with a new activated sludge process, and new final clarifiers. The system also included a new air lift pump station, dissolved air flotation process, and a new Autothermal Thermophilic Aerobic Digestion (ATAD) system. Future phases include replacement of grit removal equipment, primary clarifier mechanisms, and a planned new ultraviolet disinfection process.

Permit compliance has always been the goal for the PIerre WWTF. Early project stages were phased to allow construction of the aeration basins and final clarifiers first as they have the most impact on the effluent quality. The ATAD system was selected due to the ease of operation and ability of the process to achieve Class A biosolids, allowing maximum flexibility with final end use of the solids. The future phases, recently bid and under design, also have permit compliance as the primary goal. Ultraviolet disinfection will provide a reliable means to maintain permit compliance for coliforms, and will also allow the City of Pierre to discontinue using chlorine gas for disinfection.