This work presents the optimization of two control strategies of the wastewater treatment plant. The control architectures are assessed from an operational costs point of view, and improved by adding an upper, supervisory level of control. The upper control level dictates the optimal set-point for the two control structures by taking into consideration the quantity of ammonia nitrogen that enters the wastewater treatment plant. The relationship between the quantity of ammonia nitrogen that enters the WWTP and the optimal setpoint was established by means of linear and polynomial interpolations. The study is based on the modified Benchmark Simulation Model No. 1 (BSM1). Two modifications were made to the BSM1. The first one is the implementation of an enhanced Activated Sludge Model No. 3. This model includes two additional processes that describe the direct growth of the heterotrophic biomass on readily biodegradable substrate, in both anoxic and oxic conditions. The 2nd modification of the BSM1 regards the secondary settler, which is considered to be reactive. The simulation results show that by using the supervisory level of control the total operational cost can be reduced with almost 15.5 %, while effluent standards are maintained.