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Quantification of groundwater recharge from precipitation in the huge sand dunes is an issue in accounting for regional water balance in the Badain Jaran Desert (BJD) where about 100 lakes exist between dunes. In this study, field observations were conducted on a sand dune near a large saline lake in the BJD to investigate soil water movement through a thick vadose zone for groundwater estimation. The hydraulic properties of the soils at the site were determined using in situ experiments and laboratory measurements. A HYDRUS-1D model was built up for simulating the coupling processes of vertical water-vapor movement and heat transport in the desert soil. The model was well calibrated and validated using the site measurements of the soil water and temperature at various depths. Then, the model was applied to simulate the vertical flow across a 3-m-depth soil during a 53-year period under variable climate conditions. The simulated flow rate at the depth is an approximate estimation of groundwater recharge from the precipitation in the desert. It was found that the annual groundwater recharge would be 11-30 mm during 1983-2012, while the annual precipitation varied from 68 to 172 mm in the same period. The recharge rates are significantly higher than those estimated from the previous studies using chemical information. The modeling results highlight the role of the local precipitation as an essential source of groundwater in the BJD. (C) 2016 Elsevier B.V. All rights reserved.