An understanding of preferential flow in the vadose zone is crucial for the prediction of the fate of pollutants. Infiltration basins, developed to mitigate the adverse effects of impervious surfaces in urban areas, are established above strongly heterogeneous and highly permeable deposits and thus are prone to preferential flow and enhanced pollutant transport. This study numerically investigates the establishment of preferential flow in an infiltration basin in the Lyon suburbs (France) established over a highly heterogeneous glaciofluvial deposit covering much of the Lyon region. An investigation of the soil transect (13.5 m long and 2.5 m deep) provided full characterization of lithology and hydraulic properties of present lithofacies. Numerical modeling with the HYDRUS-2D model of water flow in the transect was used to identify the effects of individual lithofacies that constitute the deposit. Multiple scenarios that considered different levels of heterogeneity were evaluated. Preferential flow was studied for several values of infiltration rates applied after a long dry period. The numerical study shows that the high contrast in hydraulic properties of different lithofacies triggers the establishment of preferential flow (capillary barriers and funneled flow). Preferential flow develops mainly for low water fluxes imposed at the surface. The role of individual lithofacies in triggering preferential flow depends on their shapes (layering versus inclusions) and their sizes. While lenses and inclusions produce preferential flow pathways, the presence of the surface layer has no effect on the development of preferential flow and it only affects the effective hydraulic conductivity of the heterogeneous transect.