The effect of natural heterogeneity on large scale solute transport in the unsaturated zone is investigated using stochastic methods. Several of the physical parameters that control flow and solute transport in the unsaturated zone are regarded as random fields. Specifically, the influence of spatial variability in recharge applied on the surface, saturated hydraulic conductivity, water content at saturation and depth to the groundwater table, on solute flux into the groundwater, is illustrated. It is shown that the prediction of solute penetration into the groundwater through the unsaturated zone is significantly affected by the natural variability in the physical parameters. A simple stochastic model for the estimation of large scale solute flux through the unsaturated zone, is provided.