Joining the European Arrowhead Project, which looks forward to a modern collaborative automation, we will present in this positioning paper the irrigation network control problems and corresponding multi-layer approach. The first layer is the hydraulic network, itself represented by a complex model obtained in coupling Shallow Water Equations for free surface flows and Lattice Boltzmann Method to get a tractable model for optimization and supervision purposes. The second layer is the heterogeneous communication network using hybrid architectures and 6LoWPAN, a unified protocol for wired and wireless sensor networks. The third layer is the optimal reactive control system, itself developed using methods from decentralized artificial intelligent systems (namely multi-agent systems). Detailed discussions of each layer with some analytical results will be described in this paper. We will outline the potential interest of the multi-layer approach, more precisely its efficiency and reliability for supervision, energy optimization and hydraulic control of complex water transportation systems.