We examined the isotopic parameters in two C3 species (Artemisia diffusa H. Krasch and Tamarix hispida Willd.) and a C4 species [Haloxylon aphyllum (Minkw.) Iljin.] growing or planted in soils with different levels of salinity in a Central Asian desert. The oxygen isotope ratios of stem water (d18Ostem) in T. hispida and H. aphyllum distributed in high-salinity zones were similar to the d18O of artesian water (d18Oartesian) and different from that in A. diffusa distributed in lowersalinity zones. This indicates that T. hispida and H. aphyllum depend on water with low salinity in the deeper soil layer, whereas A. diffusa depends on water in the shallower soil layer that would be affected by salt accumulation. The carbon isotope composition of leaf organic matter (d13Com) and oxygen isotope enrichment in leaf organic matter above stem water (D18Oom) were lower in A. diffusa than in the other species. The responses of d13Com and D18Oom to soil salinity observed for T. hispida suggest that the species decreased its transpiration rate and increased its intrinsic water-use efficiency in response to increasing soil salinity. The d13Com and D18Oom of H. aphyllum were higher than those of the C3 species, and were not correlated with soil salinity, suggesting that H. aphyllum reduced its salt uptake by decreasing transpiration—even though it was able to access less saline water in the deeper soil layer. These results indicate that the water-use strategy of desert plants in high-salinity environments can be assessed based on their carbon and oxygen isotope ratios.