Fast sea transportation of passengers must considered safety and comfort requirements. Due to waves, there are heaving and pitching motions. These motions originate sea-sickness and can have negative effects on the ship. By means of submerged actuators, vertical motions can be smoothed. This paper considers the real case of a fast ferry with a T-foil and flaps. These actuators should move to counteract the effect of each wave. This is a control problem that also has to consider cavitation and possible fatigue of the actuators’ system. In consequence there is a multiobjective optimization problem, controlling a non-linear system., A Multiobjective Genetic Algorithm is designed and applied to the case. The research obtains satisfactory results.