Populus euphratica, as the dominant species in arid desert area, plays an important role in maintaining the stability of desert ecosystem. However, P. euphratica water-use characteristics at different sizes and the effects of flooding and groundwater depth on water use remain unclear. In this study, the hydrogen and oxygen isotope compositions of xylem water, soil water, and floods were measured and coupled with the MixSIAR model to investigate the water-use patterns of P. euphratica at different sizes, flood periods (before, during, and after floods), and groundwater depths in the Taklimakan Desert hinterland. The carbon isotope composition of P. euphratica leaves was determined to investigate the water-use efficiency (WUE) of P. euphratica. The water-use patterns of P. euphratica at different sizes were consistent because of its reproductive mode (aswxual root tiller reproduction). P. euphratica showed a greater degree of ecological plasticity during different flood periods. Before the flood, the main water sources for P. euphratica were deep-soil-layer (140–220 cm) and near-groundwater-layer (220–300 cm). During the flood, it could absorb the flood directly, reducing water absorption from deep-soil-layer and near-groundwater-layer. After the flood, it resumed water absorption from deep-soil-layer and near-groundwater-layer. P. euphratica water absorption patterns differed at different groundwater depths. In the shallow and middle groundwater depth sample plots, the water sources were the deep-soil and near-groundwater layers, and the population of P. euphratica grew well. In the deep sample plot, water absorption was mainly near the groundwater layer, and the P. euphratica population showed a decreasing trend, further explaining the degradation of P. euphratica in terms of water-use patterns. WUE is related to the growth stage of P. euphratica and the water conditions of the living environment; the more mature the P. euphratica, the more deficit the water conditions, and the higher the WUE. This study provides a basis for maintaining the stability of P. euphratica forests in arid deserts and for water allocation.