This paper presents two optimal control strategies developed for the control of two biological sequencing batch reactors (SBR), the first one performing both organic carbon and nitrogen removal from dairy wastewaters, while the second one treats toxic wastewaters. The proposed control laws are based on models that have been validated with real data acquired on two real biological SBR pilot plants. These models are presented in D. Mazouni et al., 16th IFAC World Congress, Prague, 5–8 July 2005. The validation results of these control strategies are presented and discussed.