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Climate variability and change impact groundwater resources by altering recharge rates. In semi-arid Basin and Range systems, this impact is likely to be most pronounced in mountain system recharge (MSR), a process which constitutes a significant component of recharge in these basins. Despite its importance, the physical processes that control MSR have not been fully investigated because of limited observations and the complexity of recharge processes in mountainous catchments. As a result, empirical equations, that provide a basin-wide estimate of mean annual recharge using mean annual precipitation, are often used to estimate MSR. Here North American Regional Reanalysis data are used to develop seasonal recharge estimates using ratios of seasonal (winter vs. summer) precipitation to seasonal actual or potential evapotranspiration. These seasonal recharge estimates compared favorably to seasonal MSR estimates using the fraction of winter vs. summer recharge determined from isotopic data in the Upper San Pedro River Basin, Arizona. Development of hydrologically based seasonal ratios enhanced seasonal recharge predictions and notably allows evaluation of MSR response to changes in seasonal precipitation and temperature because of climate variability and change using Global Climate Model (GCM) climate projections. Results show that prospective variability in MSR depends on GCM precipitation predictions and on higher temperature. Lower seasonal MSR rates projected for 20502099 are associated with decreases in summer precipitation and increases in winter temperature. Uncertainty in seasonal MSR predictions arises from the potential evapotranspiration estimation method, the GCM downscaling technique and the exclusion of snowmelt processes.