This paper presents the design of a Model Predictive Control (MPC) for the Calais canal, located in the north of France for satisfactory management of the system. To estimate the unknown inputs/outputs arising from the uncontrolled pumps, a Digital Twin (DT) in the framework of a Matlab-SIC 2 is used to reproduce the dynamics of the canal, and the real database corresponding to a period of three days is employed to evaluate the control strategy. The canal is characterized by two operating modes due to high and low tides. As a consequence of this, time-varying constraints on the use of gates must be considered, which leads to the design of two multi-objective control problems, one for the high tide and another for the low tide. Furthermore, a moving horizon estimation (MHE) strategy is used to provide the MPC with unmeasured states. The simulation results show that the different objectives are met satisfactorily.