This work presents the design of a hierarchical control and state estimation approach for the optimal water level management of open-channel systems using gates and pumping stations as actuators. Each reach may be characterized by a different time delay and a different prioritization of objectives. The design is divided in three layers: the upper layer determines the current operating mode. The intermediate layer is concerned with the design of appropriate controllers and observers to compute the references. Finally, the lower layer solves a scheduling problem to minimize the error between the references and the applied controls by discrete actuators. Simulation of a realistic case study based on part of the inland waterways in the north of France is used to demonstrate the effectiveness of the proposed approach.