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Wetlands are sensitive indicators of climate change and have a profound impact on the supply of water resources in surrounding areas. In this study, the hydrochemical, isotopic characteristics (δ¹⁸O and δ²H) of groundwater and surface water (lake, reservoir, and river) in the Ebinur Lake Watershed, northwestern China, were investigated to reveal the relationships between various water bodies. The results suggest that the groundwater is alkaline and has pH and total dissolved solids (TDS) values less than those of surface water. Ca²⁺ and SO₄^2− are the major ions in the groundwater and river water, whereas lake water and reservoir water are enriched in Na⁺ and SO₄^2−. With the decrease in elevation, both groundwater and river water are affected by carbonate dissolution at high elevation and by evaporitic rock dissolution at low elevation; thus, the water surrounding Ebinur Lake is subjected to runoff affected by intense evaporation−dissolution of evaporitic rocks. The stable isotope compositions suggested that the upstream part of the river is recharged by glacial meltwater from high mountains, whereas the middle−downstream parts of the river are recharged by low-elevation precipitation. Shallow groundwater and reservoir water are mainly recharged by river water and are more enriched in the downstream part of river. Water samples were also classified according to different indices, such as chemical oxygen demand (COD), NH₃-N, volatile phenol, sulfate, Zn, Co, Cu, total hardness, and Cr⁶⁺, and results showed that most groundwater is suitable for drinking and irrigation purposes. Except for Cr⁶⁺, the metal concentrations are within permissible limits. However, both groundwater and reservoir water are affected to some extent by nearby rivers from anthropogenic activity.