Groundwater recharge is primarily influenced by land use and climate. Nevertheless, it is the flow and transport processes that take place in the vadose zone that ultimately control the quantity and quality of groundwater replenishment. Vadose zone monitoring systems (VMSs) were implemented under agricultural fields. The VMSs provided continuous information on both the temporal variation in water content and the chemical composition of the sediment pore water at multiple depths in the deep vadose zone (∼20 m). Models for vertical unsaturated flow and chloride transport were calibrated to the transient data. The calibrated models were then used to investigate the temporal characteristics of groundwater recharge coupled with chloride fluxes under a crop field and a grapefruit orchard. Examination of the transient data obtained under the two sites provided insight into the percolation processes and solute mobility in the deep vadose zone. Model simulations resulted in average recharge fluxes of 131 mm yr−1 under the orchard and 199 mm yr−1 under the crop field, even though average annual water input into the irrigated orchard was 2.6 times higher than that into the crop field (rainfed). The model also predicted a 44% drop in average recharge, as well as significant chloride accumulation in the vadose zone as a consequence of a reduction of 19% in rain following climate change scenarios in the area.