The proportions of water sources in plants are related to plant adaptation, and reflect the mechanisms of niche differentiation and diversity in arid desert regions. At present, traditional physical methods is hard to determine the proportions of water sources in plants. But, due to the stable isotopes does not existed fractionation when it transported from the roots to the leaves, the stable hydrogen-oxygen isotope content (δ¹⁸O and δD) were essentially unchanged among roots, xylem, and the water sources. This resulted in the hydrogen-oxygen stable isotope analysis as a tool for accurately identifying the proportions of water sources in plants. In the present study, δ¹⁸O of the xylem of 14 dominant desert species in 8 families (including Apocynaceae, Chenopodiaceae, Tamaricaceae, Leguminosae, Salicaceae, Zygophyllaceae, Compositae and Polygonaceae), river water, groundwater, and 4 layers soil water (including 0-40, 40-70, 70-100, and 100-150 cm) were measured respectively in desert, riparian forest, salt marsh, and sand dunes of Ebinur Lake Wetland Nature Reserve, Xinjiang, China. Based on the roots distribution and δ¹⁸O, 14 dominant desert species were firstly classified into 13 deep-rooted species and 1 shallow-rooted species, and then the proportions of water sources in plants, the differences of water utilization strategies between the deep- and shallow-rooted plants, and the replenishment relationships among water sources were analyzed. The results showed that:(1) the proportions of water sources in plants were different among species and families in the Ebinur Lake Wetland Nature Reserve; (2) groundwater occupied the largest proportion in water sources in plants, whereas the 0-40-cm layer soil water was rarely used; (3) the proportions of water sources in plants differed between deep- and shallow-rooted plants. Groundwater and river water were the main sources for deep-rooted plants, whereas the soil water was the primary source for shallow-rooted plants; (4) groundwater contributed to river supply, and subsequently, these two waters were discharged into the soil waters from deep to shallow soil layers; (5) atmospheric condensed waters as a special precipitation in arid desert, to some extent, it also discharged into the soil water, river water and groundwater. Overall, in the arid desert region, the diversity of availability in water sources showed a large variation in the proportions of water sources in plants among species and families. Additionally, under the comprehensive influences of the distance from habitat to riverbank, groundwater levels, and soil salinization levels, the perennials and halophytes mainly absorbed the groundwater, river water, and deep soil water. On the contrary, the annuals and ephemeral plants utilized all water sources that could be reached and absorbed by their roots.