Density-dependent flow occurs in areas where high-salinity, denser groundwater interacts with low-salinity and less dense groundwater to create a brine-to-freshwater interface. Northern Chile’s Salar de Atacama (SdA) exhibits an exceptionally shallow interface when compared to previous density-driven modeling attempts of the basin. We therefore investigate the impact of subsurface heterogeneity on an interface’s geometry and response to changes in recharge. Site-specific 2-D models of the interface in the southeastern region of SdA, with interpretations of the area’s hydrostratigraphic framework, provide an analysis for the density-driven flow that influences the geometry of the brine-to-freshwater interface that has developed in the region. A separate equally probable series of distributions of hydraulic conductivity using a geostatistical approach is based on geologic core data from SdA and provides a means for expanding analysis to other similar arid salar (“salt flat”) environments. The study includes three groups of realizations of hydraulic conductivity distribution with 50 realizations in each group. Each group varies in the length of continuity of hydrostratigraphic units, with equal continuity between the horizontal and vertical directions in the first, increased horizontal continuity by a factor of two in the second group, and increased horizontal continuity by a factor of three in the third. Changes in hydrologic conditions are introduced to each realization and the interface’s response is subsequently assessed. Metrics for evaluation include migration rate, change in the interface’s areal extent, change in interface slope, and the response rate following the introduction to a perturbation in the aquifer’s hydrology. Model analyses indicate that evaporation rates decrease the interface’s dip and sensitivity despite changes in hydrologic and geologic conditions. Increased continuity of high-permeability pathways also decreases interface slope; increasing continuity also decreases interface stability in terms of time required to reach a new steady state. These results suggest that subsurface heterogeneity is an important but often overlooked aquifer characteristic for simulating and predicting saline intrusion risks.