Salar de Atacama (SdA) located in Northern Chile is home to one of the planet’s largest salar systems and lithium resources. Managing groundwater resources in salars is not obvious due to the lack of scientific understanding on the connectivity between the freshwater and brine systems. Using heat as a tracer in SdA provides a cost-effective method to further investigate groundwater flow in salars. This study employs 372 temperature-depth profiles from 90 boreholes between 2013-18 to understand the distinct thermal zones and flow between them in SdA. Three thermal zones exist within the southern margin of SdA’s thermal regime, at higher elevations alluvial fans containing freshwater have a temperature range between 23-28 °C. Down-gradient 2.5 km into the salar transition zone, characterized by freshwater lagoons and newly formed carbonates, the temperature range decreases to 12-17 °C. The transition zone, adjacent to the mature halite crust which hosts a lithium bearing brine and ranges in temperature from 18-22 °C. A 2D numerical groundwater and heat flow model was created to test three hydrologic scenarios to determine how the currently observed thermal regime exists and what the role of groundwater flow is between the different thermal zones. Results demonstrate that a focused flow concept matches current thermal observations with warm inflowing water discharging into the transition zone, cooling due to evaporation, reinfiltrating and preferentially flowing near the surface and discharging again at lagoons near the halite nucleus. Initial focused flow models had the halite nucleus and transition zone hydraulically connected, but results displayed advective flow between the two zones and the halite nucleus carried too much heat from current observations. Indicating the halite nucleus and transition zone has minimal connection, otherwise advective flow would result in thermal equilibrium and a lack of distinct zones as observed. Proper interpretation of temperature-depth profiles along with 2D models place critical constraints on the connectivity between the brine and freshwater systems, providing insight into salar surface energy budgets and a more comprehensive understanding of groundwater flow in the southern margin of SdA. This work gives a new perspective on the groundwater system in SdA while also contributing a novel case study to using heat as a tracer in salar systems.