The need to understand and simulate hydrological phenomena and their interactions, and the impact of anthropogenic and climate changes on natural environments have promoted the study of evaporation from bare soils in arid climates. In closed Altiplano basins, such as those encountered in arid and hyper arid basins in northern Chile, evaporation from shallow groundwater is the main source of aquifer depletion, and thus, its study is crucial for water resources management. The objective of this work is to understand the mechanisms of evaporation in saline soils with shallow water tables, in order to better quantify evaporation fluxes and improve our understanding of the water balance in these regions. To achieve this objective, a model that couples fluid flow with heat transfer was developed and calibrated using column experiments with saline soils from the Huasco salt flat basin, Chile. The model enables determination of both liquid and water vapour fluxes, as well as the location of the evaporation front. Experimental results showed that salt transport inside the soil profile modified the water retention curve, highlighting the importance of including salt transport when modelling the evaporation processes in these soils. Indeed, model simulations only agreed with the experimental data when the effect of salt transport on water retention curves was taken into account. Model results also showed that the evaporation front is closer to the soil surface as the water table depth reduces. Therefore, the model allows determining the groundwater level depth that results in disconnection of liquid fluxes in the vadose zone. A sensitivity analysis allowed understanding the effect of water-flux enhancements mechanisms on soil evaporation. The results presented in this study are important as they allow quantifying the evaporation that occurs in bare soils from Altiplano basins, which is typically the main water discharge in these closed basins. Copyright (C) 2016 John Wiley & Sons, Ltd.