In arid ecosystems, vegetation controls water and nitrate movement in the soil, reducing solute transport to aquifers. Here we analyzed nitrate distribution and transport throughout the soil profile and to the groundwater under different ecologic (vegetation type) and topographic (upland/lowland) situations across sand dune ecosystems with shallow water tables, subject to domestic grazing in the Monte desert. Based on vertical nitrate distributions in deep soil profiles we found that dune uplands (deep groundwater, low productivity) lost relatively more nitrogen than lowlands (shallow groundwater, high productivity), likely reinforcing productivity contrasts along these topographic positions. The traditional practice of nighttime animal concentration in corrals may affect nitrogen transport, with poorly vegetated interdunes at livestock posts showing higher subsoil nitrate concentrations than a well-vegetated nonsettled interdune. Vegetation left its imprint on the vertical distribution of nitrate, as suggested by the presence of a depletion zone that matched the depth of maximum root densities, followed by an underlying zone of accumulation. To explore how nitrogen exports to groundwater could affect water quality and nutrient supply to phreatophyte plants, we characterized groundwater flow patterns based on a potentiometric map and sediment characteristics, and measured groundwater electric conductivity, nitrate and arsenic concentration, and stable isotopes across 29 wells (5.8–12 m deep). Under the present land use and climate conditions, nitrate leaching does not seem to have an important and widespread effect on water quality. Nitrate concentration exceeded established limits for human consumption (45 mg L−1) in only one well, while arsenic concentration exceeded the established limits (10 μg L−1) in all but one well, reaching extreme values of 629 μg L−1. Yet, our analysis suggests that nitrate exports from corrals can reach the aquifer in localized areas and be transported to the surrounding vegetation in a relatively short time. Vegetation access to groundwater could allow ecosystems to recover part of this nutrient loss, buffering the effects of land use.