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In groundwater of the Trans-Pecos region of West Texas, unexpectedly high levels of nitrate (NO3 (-)) are documented in four basins: Red Light Draw, Eagle Flats, Wild Horse and Michigan Flats, and Lobo and Ryan Flats. NO3 (-) concentrations are changing over time in the majority (82.8 %) of wells and are increasing in most (69.8 %). The temporal change raises questions about the potential sources of NO3 (-) and about flow dynamics in these basins. Presence of NO3 (-) and temporal variability in concentration has implications beyond contamination risk because it indicates relatively rapid recharge (< 60 years) to the basin groundwaters which was not expected based on previous estimates from chloride mass balance models and groundwater age-dating techniques. This research combines existing data ranging back to the 1940s with data collected in 2011 to document a multi-decadal trend of overall increasing NO3 (-) concentration in deep basin groundwaters. Chlorofluorocarbon analyses of groundwater collected during 2011 indicate the presence of young (< 70 years) water in the basins. The authors infer from these data that there are mechanism(s) by which relatively rapid and widespread recharge occurs on the basin floors; that recharge is spatially and temporally variable and that it results from both anthropogenic (irrigated agriculture) and natural (precipitation) sources. In light of these observations, fundamental conceptual models of flow in these basins should be re-evaluated.