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Description: Rates of water discharge often exceed groundwater recharge in arid catchments. This apparent mass imbalance within a catchment may be reconciled through either regional-scale groundwater flow between topographic drainages and/or the draining of stored groundwater recharged during pluvial periods. We investigate discrepancies in the modern hydrologic budget of catchments along the west flank of the Andes in northern Chile (21–25° S), focused on the endorheic Salar de Atacama basin, and adjacent basins. Our new, uncertainty bounded, estimates of modern recharge rates do not come close to balancing observed modern groundwater discharge within topographic catchments. Two geologically realistic conceptualizations of hydrogeologic catchments discharging to Salar de Atacama were explored with a 2D groundwater model. Results from models support the interpretation that both regional flow and transient drainage of groundwater from storage are required to balance water budgets along the plateau margin. The models further examine whether this system is still responding to climatic forcing from pluvial periods and highlight general characteristics for similar plateau margin systems including: (1) water level changes at the plateau margin are highly sensitive to changes in recharge on the plateau, (2) extent and magnitude of the changes in water table are controlled by the distribution of hydraulic conductivity at the margin, (3) contributing area to the lower elevation catchment is itself dynamic, and not coincident with the topographic boundary, and (4) difficulty in reconciling the modern position of “the water table” on the Andean plateau with the regional groundwater flow conceptualization and modern discharge to low lying catchments.