A coupled sedimentary and hydrogeological model is used to quantify the impact of sedimentary heterogeneities and sinuosity on groundwater fluxes in an alluvial plain deposited by a meandering fluvial system. A 3D heterogeneous alluvial plain model is built with the stochastic/process-based model FLUMY, that simulates the evolution and the sedimentary processes of a meandering channel and its associated deposits. The resulting sedimentary blocks are translated in terms of hydrodynamic parameters (hydrofacies) and used in the 3D transient fully coupled heat and water transport model METIS. The simulated domain is 10 m-thick and at a pluri-kilometric horizontal scale, allowing considering several meanders. A head gradient is imposed at the upstream and downstream limits of the domain. The river is considered as a constant-head boundary that decreases linearly along the channel centerline. A zero-flux condition is prescribed on the other boundaries. Several cases are studied, including different degrees of sinuosity and different configurations of sediment heterogeneity: (i) a homogeneous sandy aquifer (ii) single mud-filled oxbow lake in a sandy porous media, (iii) several mud-filled oxbow lakes in a sandy porous media, and (iv) “fully” heterogeneous alluvial plain including fine-grained overbank deposits, sandy point bars, mudplugs and sandy crevasse spalys. We quantify the exchange rates and directions between the river and the aquifer along the channel centerline, the piezometric evolution and the water residence time in the heterogeneous alluvial plain. This original method can improve our understanding of the functioning of alluvial corridor and evaluate the relevance of taking into account the structural heterogeneity of alluvial plains in larger regional hydrogeological models.