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The Upper San Pedro River Basin (Southeastern Arizona, United States) contains one of the few desert riparian areas in the Southwest, a system that is dependent on both shallow groundwater to support phreatic vegetation and baseflow for aquatic plants and animals. Proper management decisions for sustaining this biodiversity hotspot require understanding the hydrology of the riparian system and its interaction with the basin aquifer. To meet this need and to assess whether the techniques used would be efficient for evaluating other semiarid riparian ecosystems, we addressed the following questions. What are the contributions of different water sources (e.g., local recharge during monsoon flood events versus inflow of basin groundwater) to riparian groundwater and river baseflow? How does the spatial variability in water sources relate to gaining and losing reaches along of the river? We first characterize the possible water sources to the riparian system using a suite of geochemical tracers. Results indicate that, of the possible sources, basin groundwater recharged along the Huachuca Mountains to the west and local recharge of monsoon floodwaters are the dominant riparian water sources. Then, using their geochemical composition, we quantify these sources using a two end‐member mixing model. We find that riparian groundwater composition varies between gaining and losing reaches. Locally recharged monsoon floodwater comprises 60 to 85% of riparian groundwater in losing reaches whereas that of gaining reaches contains only 10% to 40%. Baseflow, sampled year round, also contains a significant component of monsoon floodwater ranging from 80% on the upstream end and decreasing to 55% after passing though several gaining reaches. These results highlight the significance of local recharge during monsoon flood events as a water source for desert riparian systems, a fact that should be addressed when constructing and calibrating hydrologic models used to evaluate these future water management decisions.

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Analysis of a typical semiarid mountain system recharge (MSR) setting demonstrates that geochemical tracers help resolve the location, rate, and seasonality of recharge as well as ground water flowpaths and residence times. MSR is defined as the recharge at the mountain front that dominates many semiarid basins plus the often-overlooked recharge through the mountain block that may be a significant ground water resource; thus, geochemical measurements that integrate signals from all flowpaths are advantageous. Ground water fluxes determined from carbon-14 ((14)C) age gradients imply MSR rates between 2 x 10(6) and 9 x 10(6) m(3)/year in the Upper San Pedro Basin, Arizona, USA. This estimated range is within an order of magnitude of, but lower than, prior independent estimates. Stable isotopic signatures indicate that MSR has a 65% +/- 25% contribution from winter precipitation and a 35% +/- 25% contribution from summer precipitation. Chloride and stable isotope results confirm that transpiration is the dominant component of evapotranspiration (ET) in the basin with typical loss of more than 90% of precipitation-less runoff to ET. Such geochemical constraints can be used to further refine hydrogeologic models in similar high-elevation relief basins and can provide practical first estimates of MSR rates for basins lacking extensive prior hydrogeologic measurements.