The efficacy of different proportions of silt-loam/bentonite mixtures overlying a vadose zone in controlling solute leaching to groundwater was quantified. Laboratory experiments were carried out using three large soil columns, each packed with 200-cm-thick riverbed soil covered by a 2-cm-thick bentonite/silt-loam mixture as the low-permeability layer (with bentonite mass accounting for 12, 16 and 19% of the total mass of the mixture). Reclaimed water containing ammonium (NH4+), nitrate (NO3−), organic matter (OM), various types of phosphorus and other inorganic salts was applied as inflow. A one-dimensional mobile–immobile multi-species reactive transport model was used to predict the preferential flow and transport of typical pollutants through the soil columns. The simulated results show that the model is able to predict the solute transport in such conditions. Increasing the amount of bentonite in the low-permeability layer improves the removal of NH4+ and total phosphorous (TP) because of the longer contact time and increased adsorption capacity. The removal of NH4+ and OM is mainly attributed to adsorption and biodegradation. The increase of TP and NO3− concentration mainly results from discharge and nitrification in riverbed soils, respectively. This study underscores the role of low-permeability layers as barriers in groundwater protection. Neglect of fingers or preferential flow may cause underestimation of pollution risk.