|Tamarix taklamakanensis, a dominant species in the Taklimakan Desert of China, plays a crucial role in stabilizing sand dunes and maintaining regional ecosystem stability. This study aimed to determine the water use strategies of T. taklamakanensis in the Taklimakan Desert under a falling groundwater depth. Four typical T. taklamakanensis nabkha habitats (sandy desert of Tazhong site, saline desert-alluvial plain of Qiemo site, desert-oasis ecotone of Qira site and desert-oasis ecotone of Aral site) were selected with different climate, soil, groundwater and plant cover conditions. Stable isotope values of hydrogen and oxygen were measured for plant xylem water, soil water (soil depths within 0–500 cm), snowmelt water and groundwater in the different habitats. Four potential water sources for T. taklamakanensis, defined as shallow, middle and deep soil water, as well as groundwater, were investigated using a Bayesian isotope mixing model. It was found that groundwater in the Taklimakan Desert was not completely recharged by precipitation, but through the river runoff from snowmelt water in the nearby mountain ranges. The surface soil water content was quickly depleted by strong evaporation, groundwater depth was relatively shallow and the height of T. taklamakanensis nabkha was relatively low, thus T. taklamakanensis primarily utilized the middle (23%±1%) and deep (31%±5%) soil water and groundwater (36%±2%) within the sandy desert habitat. T. taklamakanensis mainly used the deep soil water (55%±4%) and a small amount of groundwater (25%±2%) within the saline desert-alluvial plain habitat, where the soil water content was relatively high and the groundwater depth was shallow. In contrast, within the desert-oasis ecotone in the Qira and Aral sites, T. taklamakanensis primarily utilized the deep soil water (35%±1% and 38%±2%, respectively) and may also use groundwater because the height of T. taklamakanensis nabkha was relatively high in these habitats and the soil water content was relatively low, which is associated with the reduced groundwater depth due to excessive water resource exploitation and utilization by surrounding cities. Consequently, T. taklamakanensis showed distinct water use strategies among the different habitats and primarily depended on the relatively stable water sources (deep soil water and groundwater), reflecting its adaptations to the different habitats in the arid desert environment. These findings improve our understanding on determining the water sources and water use strategies of T. taklamakanensis in the Taklimakan Desert.