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.Water 2019, 11, 687 2 of 17 managed aquifer recharge [11]; and, the most concerning, its use for irrigation. Unease has emerged due to the lack of the major nutrients, namely, calcium, magnesium, and sulfur, in desalinated seawater [12]. Half of the irrigation water in Israel is treated wastewater. The relatively low content of calcium and magnesium in desalinated water and the high addition of sodium in household use has raised concerns about the high sodium adsorption ratio (SAR) in wastewater originating from desalinated seawater [13].In contrast to the aforementioned concerns, the change towards lower salinity irrigation water may be regarded as an opportunity. Higher yields or smaller irrigation rates for the same yield and reduced leaching of salts below the roots are expected benefits of using more desalinated water for irrigation [14,15]. This study aims at showing that the use of low-salinity water for irrigation can also reduce the nitrate leaching to groundwater (the greatest groundwater pollution related to agriculture in Israel and worldwide, [16]). It is hypothesized here that under cropped conditions, low-salinity irrigation water may reduce nitrate leaching below the root zone, due to two mechanisms: (i) decreasing vertical water fluxes and (ii) increasing nitrogen uptake by plant roots when the latter process is affected by the competition between chloride and nitrate [17].The general objective of the present study was to investigate the effect of the irrigation water quality (salinity) on water uptake and nitrogen uptake by the plants' roots, and on the nitrate and the chloride mass fluxes below the root zone. Considering cropped conditions, the specific objective of this...