The Propopis tamarugo Phil, also known as Tamarugo, is an endemic and protected tree that survives in the Atacama Desert—a hyper arid and highly saline environment. The Tamarugo is threatened because of groundwater overexploitation, and its preservation depends on the soil moisture in the vadose zone, as many of the tree roots do not reach the current water table levels. To improve the estimation of soil moisture available for the Tamarugo trees, we applied a hydrogeological model that couples the unsaturated and saturated zones. The model was used to represent different groundwater exploitation and recharge scenarios between February 2006 and September 2030 to predict simultaneously groundwater levels and soil moisture. The model results show that even at locations where water table depletion is relatively small (~1–1.5 m), soil moisture can drastically decrease (0.25–0.30 m3/m3). Therefore, Tamarugo survival can be better addressed, as the applied model provides a management tool to estimate response of Tamarugo trees to changing soil moisture. To further improve the model and its use to assess Tamarugo survival, more field data, such as soil hydrodynamic properties and soil moisture, should be collected. Additionally, relationships between the state of the Tamarugo trees and soil moisture should be further constructed. In this way, the developed model will be able to predict future conditions associated to the Tamarugo’s health state.