In arid and semi-arid environments, desert vegetation plays an important role in preventing soil erosion by wind and helps maintain the stability of desert and oasis ecosystems. Four types of typical desert vegetation, namely Populus euphratica, Haloxylon ammodendron, Nitraria sibirica, and Halostachs caspica, corresponding to different habitats (i.e., river bank, sand dune, desert, and salt marsh) were chosen as the model vegetation in this research. The δ2H and δ18O for rainwater, soil water, and plant water were applied to identify the water sources and quantify the proportions of different water sources used over the entire plant growth period (from March to October). The results showed that the precipitation δ2H and δ18O in the Ebinur Lake basin varied from -142.5‰ to -0.6‰ and from -20.16‰ to 1.20‰, respectively. The largest δ2H and δ18O values occurred in summer and the smallest in winter. The soil water δ2H and δ18O of the four habitats decreased gradually with increasing depth. The δ2H and δ18O values of water extracted from the stems of the four plants had similar variation trends, that is, the maximum was observed in spring and the minimum in summer. Among the four plants, H. caspica had the highest stable isotopic values in the stem water, followed by N. sibirica, H. ammodendron, and P. euphratica. The water sources and utilization ratios of desert vegetation varied across different growth stages. Throughout the growing period, H. ammodendron mainly used groundwater, whereas the water source proportions used by N. sibirica varied greatly throughout the growing season. In spring, plants mainly relied on surface soil water, with a contribution rate of 80%-94%. However, in summer, the proportion of deep soil water used was 31%-36%; and in autumn, the proportion of middle soil water used was 33%-36%. H. caspica mainly relied on topsoil water in spring and autumn, and the proportion of soil water in the middle layer slightly increased to 20%-36% in summer. P. euphratica mainly used intermediate soil water in spring with a utilization rate of 53%-54%. In summer, groundwater was the main source, with a utilization rate of 72%-88%, and only 2%-5% came from river water, whereas in autumn, the river water utilization rate rose to 11%-21%. The results indicated that there were significant differences in water use sources during the growing period for desert vegetation in arid areas. This research provides a theoretical basis for understanding water use mechanisms, water adaptation strategies, and vegetation restoration and management in arid areas.