In this paper, the problem of flooding management using hybrid model predictive control is presented and applied to the Ebro River in Spain. The Ebro River presents flooding episodes in the city of Zaragoza during spring when snow melts in the Pyrenees. To avoid flooding in populated areas, some land outside the city is prepared for flooding. This paper presents a control approach to determine and fix the level of flooding in pre-established zones by controlling side gates that determine the water input to the land to be flooded. Finally, several scenarios are used to validate the performance of the proposed approach.