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Accurate estimation of groundwater evapotranspiration (ETG) is the key for regional water budget balance and ecosystem restoration research in hyper-arid regions. Methods that use diurnal groundwater level (GWL) fluctuations have been applied to various ecosystems, especially in arid or semi-arid environments. In this study, groundwater monitoring devices were deployed in ten lake basins at the hinterland of the Badain Jaran Desert, and the White method was used to estimate the ETG of these sites under three main vegetation covers. The results showed that regular diurnal fluctuations in GWL occurred only at sites with vegetation coverage and that vegetation types and their growth status were the direct causes of this phenomenon. On a seasonal scale, the amplitudes of diurnal GWL fluctuations are related to vegetation phenology, and air temperature is an important factor controlling phenological amplitude differences. The estimation results using the White method revealed that the ETG rates varied among the observation sites with different vegetation types, and the months with the highest ETG rates were also different among the sites. Overall, ETG was 600∼900 mm at observation sites with Phragmites australis during a growing season (roughly early May to late October), 600∼650 mm in areas with Achnatherum splendens, and 500∼650 mm in areas with Nitraria tangutorum and Achnatherum splendens. Depth to water table and potential evapotranspiration jointly control the ETG rates, while the influence of these two factors varied, depending on the specific vegetation conditions of each site. This study elucidated the relationship between diurnal GWL fluctuations and vegetation in desert groundwater-recharged lake basins and expanded the application of the White method, providing a new basis for the calculation and simulation of regional water balance. [ABSTRACT FROM AUTHOR]