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Evapotranspiration (ET) including evaporation from soil surfaces and transpiration through plants’ stomata exerts dominant controls on shallow groundwater dynamics under hyper-arid climates. Our analyses of diurnal and seasonal groundwater dynamics at desert sites in northwestern China for the period 2010-2014 showed that different patterns of groundwater dynamics in a Gobi-desert and riparian zones are highly related to ET processes. To quantify ET in the hyper-arid climates, we developed diagnostic indicators of the groundwater-ET relationship and a methodology based on seasonal groundwater level fluctuation approach. Under similar climates and depth to the water table (2-2.5 m), ET in the riparian zones as a result of direct root water uptake (RWU) through riparian shrubs (0.63-0.73 mm/d at the Tamarix ramosissima site and 1.89-2.33 mm/d at the Populus euphratica site) is much greater than that in a Gobi-desert site (0.12-0.27 mm/d). Numerical simulations using a one-dimensional land surface model with a RWU model that explicitly describes root-groundwater interactions indicate that direct RWU at the riparian sites is primarily dependent on the root dynamics that interacts with groundwater dynamics.