The hydraulic management of the Rhine has drastically modified the hydrological functioning of alluvial zones and caused the disconnection of most side-channels of the Rhine and alluvial forests. The re-flooding restoration works of the disconnected sectors are planned with objective of both the retention of flood and of ecological flooding which should allow these zones to recover all or part of their functionality.The Erstein polder is a forested experimental area for monitoring the impact of the alluvial zones re-flooding. The flooding of the Rhine plain may modify its hydrological functioning in terms of runoff, groundwater-river exchanges and groundwater recharge. Our general objective is to analyze and quantify water flux in an unsaturated porous aquifer. Therefore, based on the given hydraulic and hydrogeological conditions of the study site, we performed numerical flow simulations using the finite element model Feflow 5.3.This work is structured in five chapters. The starting point is a state of the art about the functioning and the structure of alluvial zones and the mechanisms of water flux in these areas. The second chapter presents the experimental site. A scientific monitoring mission has been implemented on the polder site and an extensive data base of hydrological measurements (surface and groundwater) was created. This data base was used to characterize the water flux in the unsaturated zone. The third chapter is devoted to the construction of the hydrodynamic model. Given the importance of the side channels network supplied by the existing groundwater inside the polder, the water exchange between surface water and groundwater was discussed. Apart from the groundwater recharge by streams, a significant infiltration of water from the soil surface during flooding contributes to groundwater recharge. To quantify this part, we developed an original approach in order to characterize the heterogeneities of soils using hydrodynamic model parameters. These heterogeneities that vary spatially on the polder have a significant influence on the vertical flow and the residence time of water from the ground surface to the groundwater. The results obtained in 1D were then used to model the influence of soil heterogeneities of the entire area of the study site on water infiltration during inundation event and groundwater recharge. Different scenarios of heterogeneity were used to render the structure of the porous aquifer progressively more complex in order to evaluate the impact of the heterogeneities on water flux in the vadose zone of the Erstein polder.