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The Salar de Atacama is one of the most well-known saline endorheic basins in the world. It accumulates the world main lithium reserves and contains very sensitive ecosystems. The objective of this work is to characterize the hydrodynamics of the Salar de Atacama, and to quantify its complex water balance prior to the intense brine extraction. The methodology and results can be extrapolated to the groundwater flow and recharge of other salt flats. A three-dimensional groundwater flow model using low computational effort was calibrated against hundreds of hydraulic head measurements. The water infiltrated from the mountains ascends as a vertical flux through the saline interface (mixing zone) produced by the density contrast between the recharged freshwater and the evaporated brine of the salt flat nucleus. This water discharges and is largely evaporated from lakes or directly from the shallow water table. On the other hand, the very low hydraulic gradients, coupled with the presence of the mixing zone that operates as barrier, leads the salt flat nucleus to act as a hydrodynamically quasi-isolated area. The computed water table shows the lowest hydraulic head in the salt flat nucleus near the discharge at the mixing zone. The groundwater balance of the Salar de Atacama in its natural regime was quantified resulting in an inflow/outflow of 14.9 m3·s−1. This balance considers the basin as an endorheic system. The very low infiltration values that are generally assumed for hyperarid basins are not consistent with the hydrogeology of the Salar de Atacama. Indeed, very high infiltration rates (up to 85% of rainfall) occur because of the high degree of fracturing of rocks and the scarce vegetation. This high infiltration is consistent with the light isotopic composition of the water from the recharge area (Altiplano). Therefore, the existence of additional inflows outside the basin is unlikely. © 2018, The authors acknowledge Sociedad Química y Minera de Chile S.A. (SQM) for their support and sharing data throughout the hydrogeological characterization of the SdA site. M.A. Marazuela gratefully acknowledges the financial support from the AGAUR (Agència de Gestió d'Ajuts Universitaris I de Recerca, Generalitat de Catalunya) and the European Union (grant number 2017FI B1 00194). Finally, we thank three anonymous reviewers for their valuable comments.

The Salar de Atacama is used as a case study to analyse and quantify coupled natural (evaporation and recharge) and anthropogenic processes (pumping of lithium-rich brine) to abstract their patterns to other salt flats using a three-dimensional groundwater flow model. Important changes in the dynamics of the water table between the pre-operational period (1986–1994) and operational period (1994–2015) are observed. The water table exhibited a gradual drawdown during the pre-operational period because the evaporation was greater than the recharge for most of these periods. This negative balance was counteracted by some sharp rises that were produced by direct rainfall events on the salt flat. The deep lateral recharge that arrived from the mountains did not produce abrupt changes in the water table because the rainfall events in the mountains were damped by the distance of the recharge zone and great thickness of the unsaturated zone. The natural evolution of the water table was modified by the intensive brine pumping that was performed in the south-western Salar de Atacama during the operational period. As evaporation depends on the water table depth, the pumping caused a drawdown of the water table, resulting in an evaporation rate reduction that partially compensated for the pumped brine in the water balance of the basin. This effect is defined as the damping capacity of salt flats. Thus, salt flats have a high capacity for dampening oscillations in their water table in response to both natural and anthropogenic disturbances which is of great importance for the management of lake and wetland ecosystems and brine exploitation. The limit of the dampening capacity of salt flats is defined by the evaporation extinction depth, which is in the range of 0.5–2 m. © 2018 Elsevier B.V., The authors acknowledge Sociedad Química y Minera de Chile S.A. for their support and sharing data throughout the hydrogeological characterization of the SdA site. M.A. Marazuela gratefully acknowledges the financial support from the AGAUR (Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya) and the European Union (grant number 2018FI B2 00068). Finally, we thank four anonymous reviewers for their valuable comments.