Pollution of groundwater by nitrate originating from irrigated fields was considered for this study. We hypothesized that under cropped conditions, low-salinity irrigation water (e.g., desalinated water) could reduce nitrate leaching below the root zone, due to two possible mechanisms: (i) decreased vertical water fluxes and (ii) increased nitrogen uptake by plant roots due to chloride-nitrate competition. The main goal of this study was to investigate this hypothesis. Considering a citrus grove, the investigation relied on three-dimensional (3-D) simulations of flow and transport in a variably saturated and spatially heterogeneous flow domain performed for three successive years. Results of the analyses suggest that the main mechanism responsible for the reduction in the nitrate leached below the root zone under irrigation with low-salinity water is the effect of the latter on the spatial distribution of the rate of water uptake by the roots. The latter, in turn, significantly reduces water content, hydraulic conductivity, and vertical velocity, and, consequently, solute mass fluxes along the soil profile. On the other hand, chloride-nitrate interaction has only a relatively small effect on the nitrate mass fluxes at relatively deep soil depths, far below the root zone, particularly when the irrigation water salinity decreases. © 2019 by the authors.