The activated sludge process is a complex microbial system used for biological wastewater treatment, i.e., carbon and ammonium removal. The main control objective is to regulate the outflow water quality despite disturbances in the inflow, such as influent flow, or influent concentration. The alternate phase process consists of a single bioreactor where oxygen is supplied intermittently to create nitrification and denitrification conditions while the biomass is recycled continuously from a settler. In this study, a switched affine model is first derived from an existing dynamic model. Then, a switching signal law and a feedback control are developed to reduce the ammonium concentration while keeping the closed-loop system stable. The proposed control strategy is validated in simulation with MATLAB/Simulink considering several influent scenarios such as dry, rainy, and stormy weather conditions.