Due to its rapid movement, preferential flow (PF) in the vadose zone allows much faster contaminant transport, which may have a significant impact on ground-water quality. PF can occur in heterogeneous vadose zones and it strongly depends on hydric and hydraulic conditions like entering flow rates at surface. This study deals with the modeling of the establishment of PF, and related solute transfer during the infiltration phase in a strongly heterogeneous glaciofluvial deposit. This deposit is made of four contrasting lithofacies (sand, gravel, bimodal gravel and matrix-free gravel) and lies underneath an urban infiltration basin (Lyon, France). Previous studies have been carried out on this site and linked the regionalization of soil pollution with the lithological heterogeneity. But none of them clearly demonstrated how heterogeneity could impact flow and solute transfer and may explain such a regionalization. In this study, we model flow and solute transfer at the trench scale for both uniform and heterogeneous profiles in order to characterize the effect of lithological heterogeneity. In addition, such a modeling was performed for two different entering flow rates to depict the influence of condition at surface on PF. A key result is that heterogeneity clearly impacts unsaturated flow and solute transfer. Numerical modeling permitted pointing out the existence of PF paths associated with the sedimentary heterogeneity of the glaciofluvial deposit. For lower surface fluxes, the sand lens and matrix-free gravel were the sources of capillary barrier effects, leading to a funneled flow and a groundwater recharge characterized by earlier and more dispersed wetting fronts. Such a flow pattern enhances solutes transfer and reduces solute retention by soil. Thus, the effect of heterogeneity on solute transfer is significant, especially for the most reactive solutes.