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Quantifying the effects of anthropogenic processes on groundwater in arid regions can be complicated by thick unsaturated zones with long transit times. Human activities can alter water and nutrient fluxes, but their impact on groundwater is not always clear. This study of basins in the Trans-Pecos region of Texas links anthropogenic land use and vegetation change with alterations to unsaturated zone fluxes and regional increases in basin groundwater NO3- concentrations. Median increases in groundwater NO3- (by 0.7-0.9 mg-N/l over periods ranging from 10 to 50+ years) occurred despite low precipitation (220-360 mm/year), high potential evapotranspiration (similar to 1570 mm/year), and thick unsaturated zones (10-150+ m). Recent model simulations indicate net infiltration and groundwater recharge can occur beneath Trans-Pecos basin floors, and may have increased due to irrigation and vegetation change. These processes were investigated further with chemical and isotopic data from groundwater and unsaturated zone cores. Some unsaturated zone solute profiles indicate flushing of natural salt accumulations has occurred. Results are consistent with human-influenced flushing of naturally accumulated unsaturated zone nitrogen as an important source of NO3- to the groundwater. Regional mass balance calculations indicate the mass of natural unsaturated zone NO3- (122-910 kg-N/ha) was sufficient to cause the observed groundwater NO3- increases, especially if augmented locally with the addition of fertilizer N. Groundwater NO3- trends can be explained by small volumes of high NO3- modern recharge mixed with larger volumes of older groundwater in wells. This study illustrates the importance of combining long-term monitoring and targeted process studies to improve understanding of human impacts on recharge and nutrient cycling in arid regions, which are vulnerable to the effects of climate change and increasing human reliance on dryland ecosystems.