In arid ecosystems, evapotranspiration generally exceeds precipitation, preventing deep drainage and groundwater recharge. We propose that vegetation changes associated with the establishment of pastoralist settlements (i.e. livestock stations) can disrupt the ecological and hydrological linkages in arid groundwater-coupled ecosystems of the Monte desert (Argentina), allowing local groundwater recharge and nitrate leaching to the aquifer, affecting groundwater quality. We tested this hypothesis by analysing vegetation, land use indicators, water and nitrate dynamics in three pairs of livestock stations and relatively undisturbed control woodlands. Livestock stations had lower vegetation and dead wood but higher dung covers than control woodlands, indicating soil and vegetation changes associated to land use. Water and nitrate dynamics were also affected by land use. Soil nitrate and water contents sampled down to the water table were higher, and soil chloride and salinity were lower in livestock stations, indicating higher water percolation and N input/transport rates. Higher groundwater nitrate concentrations in livestock stations indicate that these areas behave as foci of N and water export from ecosystems to the phreatic aquifer. Our study supports the idea that vegetation in arid areas prevents downward surface–groundwater interactions, but it also indicates that human modifications of vegetation disrupt this control, reducing soil water consumption and allowing vertical movement of water and solutes to the aquifer, which can modify groundwater quality. Disruptions of ecological processes by livestock activities clearly affect the hydrological links between surface and groundwater. Copyright © 2013 John Wiley & Sons, Ltd.