The spatiotemporal structure of wind-driven circulation patterns and associated water exchanges can drive important bio-hydrodynamic interactions in shallow lagoons. The Vaccares lagoon system is a complex shallow hydrosystem located in the central part of the Rhone Delta (France). It is internationally recognized as part of a biosphere reserve within the framework of UNESCO's Man and Biosphere Programme, and as a RAMSAR site. Due to its frequent occurrence in this area, and considering the shallowness of the Vaccares lagoon system, wind is assumed to play a major role in the hydrodynamic and biological processes. In this study, a hydrodynamic model was developed to investigate the structure of wind-driven circulations in the Vaccares lagoon system, to provide insights into their role in transport and water exchange processes. The implementation and assessment (calibration and validation) of the model is presented first. Simulations were then performed for two typical steady wind conditions and for one measured unsteady wind event. The results illustrate the influence of the complex geometry of the Vaccares lagoon system on the wind-driven circulations, and the differences observed between the different sub-lagoons in this system. The differences in wind-induced water exchanges between these sub-lagoons are also discussed.