Optimal aeration control strategies for sequencing batch reactors in WWT with bypass nitrification are hereby studied. The operation is defined alternating aerobic and anoxic phases with high frequency. The controlled variable, the aeration, can only adopt fixed values, on and off, leading to a discrete trajectory of bang-bang type. The problem is to compute the number of switches and individual length of each aerobic and anoxic stage. This leads to a mixed integer nonlinear optimal control problem (MINTOC). The solution is challenging, since both integer and continuous variables ought to be considered in the optimization. In contrast to previous work, where optimization is performed based on the separation and independent solution of the integer and continuous problem, we apply an algorithm originally proposed by Sager (2005). The optimization program minimizes operation time and energy consumption. Effluent concentrations are considered as nonlinear constraints in accordance to environmental regulations. (C) 2014 Elsevier Ltd. All rights reserved.