This paper deals with the optimal control of membrane fouling allowing the maximization of the total water production of a MBR system over a given period of time. The main objective is to find the optimal switching sequence of filtration and backwash cycles that mitigates membrane fouling and maintains a good performance of the process. The key contribution of our work is in the synthesis of a generic and robust optimal control that can be applied in practice to a large number of different MBR processes.