Abstract : Whether during floods or during low flow regimes, one of the main challenge of real-time river basin management is to prevent crises, generally defined by crossing flow thresholds at different strategic points, in order to limit economic, ecological, material and human damage. The thesis proposes a methodology for synthesis and identication of a model which simulates flows, incorporating hydraulic transfers (propagation in a river stretch), hydrologic transfers (transformation of rainfall into runoff), and withdrawals in the case of low flows. The model is built under operational constraints, such as robustness against uncertainties, real-time data assimilation or automatic control of reservoirs. It is described by a semi-distributed coupling between a hydraulic module based on simplified physics, and a global and conceptual hydrological module. The approach is validated through various theoretical examples and applications on real cases : transfer in a river stretch subject to tidal inuence, synthesis of an open-loop controller on an irrigation canal, simulation of flows at the outlet of various French watersheds, flood forecasting, synthesis of state observers for the reconstitution of withdrawals.