This paper presents a switched linear system representation of water canal dynamics to incorporate different operating modes, which arise due to the occurrence of extreme weather phenomena such as flooding and drought episodes. To guarantee the stability during mode switching, a proper analysis on permanence regions-given by a collection of equilibrium states-for the switched linear system is presented. The permanence region is computed within a compact set, which depends on an adequate level region for the canals. A suitable algorithm is used to formulate an asymptotic stable Model Predictive Control (MPC) that steers and maintains the states of the system inside the target region indefinitely in a feasible manner. This strategy is successfully tested in a simulation using a realistic model of a canal.