Two-level controllers for dissolved oxygen reference trajectory tracking for activated sludge processes is proposed and investigated. Both the nutrient and the phosphorous removal from a wastewater by its biological treatment using an activated sludge technology are considered. Typically, an aeration system itself is a complicated hybrid nonlinear dynamical system with faster dynamics compared to internal dynamics of the dissolved oxygen at a biological reactor. It is common approach to neglect this dynamics and also important operational limitations of this system such as a limited frequency of allowed switching of the blowers The paper proposes a two level controller to track prescribed dissolved oxygen trajectory. The upper level control unit produces desired aeration flow set points. For this unit the aeration system is an actuator. The nonlinear model predictive control algorithm is applied to design this controller unit. Also, the predictive control is used to design the lower level control unit based on a linearised hybrid dynamics of the aeration process. The overall controller is validated by simulation using real data sets and ASM2d model of the biological reactor.