Many control strategies can be found in literature for controlling a river system. Most of these methods focus on set-point control such that the most upstream or downstream part of each reach tracks a certain reference trajectory while minimizing the effect of disturbances. However many of the control techniques suitable for set-point control cannot be used at the same time for preventing a river from flooding when large disturbances take place. In this paper we show that Model Predictive Control can be used for set-point control and flood control of a river system consisting of two reaches and one gate. For this we use a linearized version of the Saint-Venant equations with special attention to the gate dynamics.