Numerical simulations of water flow and solute transport were used to investigate the effect of the recharge (rain/irrigation) at the soil surface on solute spreading and breakthrough in a realistic, three-dimensional, heterogeneous, vadose zone–groundwater flow system. Results of the analyses suggest that smaller recharge at the soil surface increases the relative variability in the response of the unsaturated flow system, decreases the groundwater recharge from the unsaturated zone, and, concurrently, decreases the degree of nonuniformity of the groundwater flow. Consequently, smaller recharge at the soil surface enhances the longitudinal and, especially the transverse spreading of the solute plume and increases the spreading of the expected solute BTC at the lower boundary of the unsaturated zone. Furthermore, smaller recharge at the soil surface decreases the extent of the vertical penetration of the solute plume into the groundwater, slows the peak arrival of the expected BTC, and considerably increases the spreading of the expected solute BTC at a given vertical control plane in the saturated region. It was shown that for the combined flow system considered here in which the solute plume is displaced to a sufficiently large vertical distance from the inlet zone at the soil surface, the variable that controls the transport is the cumulative recharge at the soil surface, and not the recharge rate.