In water-stressed hyperarid basins, questions mount over the impacts of anthropogenic groundwater extraction and climate-driven perturbations on groundwater-surface water interactions and the resilience of ecosystem-critical surface waters. Since high rates of evaporation often outpace recharge to such basins and therefore cause the formation of brines, these surface waters are also unique because density-driven flow causes the upwelling in fresh groundwater and discharging along both the transition zone between freshwater and brine. Coupling groundwater with surface water observations from Sentinel-2 data in Salar de Atacama provides an unprecedented opportunity to evaluate surface water inundation patterns following extreme precipitation events, elucidating two surface water types with distinct inundation patterns: terminal pools located in the transition zone have high recession rates whereas transitional pools located at the boundary of full brine have lower recession rates. Lumped parameter modeling further provides an opportunity to define the inflow and outflow components that control inundation patterns in the surface water bodies. Results indicate that groundwater discharge controls inundation patterns for surface water bodies that reside on the margins of the basin floor. Extending these observations to the wider Altiplano-Puna region, both inundation records from Sentinel and Landsat satellite missions provide insight on both short and long-term dynamics, respectively. Coupling these records with climate data and remotely sensed variations in vegetated area, both regional and local trends emerge which further insight the importance of aquifer storage and groundwater discharge providing key inflow to surface water. A complicating and evolving factor which may influence groundwater-surface water interactions is mineral precipitation-dissolution reactions and resulting changes in the hydrogeologic properties of salar-bearing aquifers. A series of reactive transport simulations through the PFLOTRAN code therefore explores the influence of reaction-induced alterations in permeability of the subsurface. Simulations indicate that these aquifers can experience permeability alterations following hydraulic perturbations which may primarily occur along the brine-to-freshwater interface and which can alter the distribution of groundwater discharge. Combined, results from these studies highlight unique hydrogeologic dynamics that influence the availability of surface water and further emphasize the importance of groundwater discharge in arid environments.