Transport and supply water networks are two types of systems which have received a significant amount of attention in the recent years. Issues on how to obtain the best performance for a given transport or supply water systems, or how to coordinate interactions between them are still open and need more research. This chapter presents a hierarchical Model Predictive Control (MPC) scheme with a supervisor that coordinates transport and supply water systems. First, a two-level hierarchical control structure resulting from a functional decomposition of water network is briefly presented. Inside each hierarchy, a MPC controller is used. In the two-level hierarchy, a supervisory coordinating mechanism is used to generate control strategies which consider objectives at different time scales. The first level, in charge of managing the transport system, works in a daily scale in order to achieve the global management policies for the transport over water (e.g., navigation, vessels and barges) in different rivers and balance management of different reservoirs. The second level, in charge of managing the supply system, works in a hourly scale and manipulates actuator (pumps and valves) set-point to satisfy the local water supplying objectives (e.g.,minimizing economic cost, handling emergency storage and smoothing actuator operation). The results of the modelling will be applied to the Catalunya Regional Water Network and based on an aggregate model.