The important exposition of ‘green mountains and clear water are as good as mountains of gold and silver’ shows that Chinese leaders attach importance to ecological environment construction. The study on the healthy and sustainable development of lakes in the arid region of Northwest China, where is short of water resource and is of a fragile ecological environment. It is an indispensable part of constructing the harmonious development of economy and environment in China. As a typical closed lake in arid area of Xinjiang, Lake Ebinur is the lowest discharge datum in this area. The unique water cycle makes it highly sensitive to climate change and human activity. In recent years, with the further large-scale exploitation of water and soil resources in the Lake Ebinur wetland and the abundant supply rivers, the ecosystem of the Jinghe River Basin has been seriously disturbed, for example, the desertification and salinization are obviously intensified, and the ecological environment is deteriorating day by day. Therefore, maintaining the water quality of the river into the lake has become an important means to maintain the water balance and the ecological environment of the Lake Ebinur. This paper made an in-depth study of mainly rivers in the Lake Ebinur Basin on October 2016, March 2017, May and July. The characteristics of hydrochemistry and hydrogen and oxygen isotopes are systematically studied. The results show that most high value of water quality indicators appeared in Bole, Wenquan, Jinghe County and near the Lake Ebinur. The main pollution is from water eutrophication, industrial and mining industry and organic matter. The pollution degree in summer and autumn is higher than that in spring and winter. There is obvious linear relationship between δ¹⁸O and δ²H, and its coefficient was as follows:summer (R²=0.99) > spring (R²=0.98) > autumn (R²=0.96) > winter (R²=0.90). The distribution of water line along the local atmosphere. Influenced by the strong evaporation of the northwest arid region, the slope of the rivers in each season is less than 8, and the d-excess value is positive. The value of δ¹⁸O in Bortala and Jinghe River shows a trend of gradual deviation along the flow. The index of correlation between hydrogen and oxygen isotopes in Bortala River and height is that spring (R²=0.70) > winter (R²=0.57) > summer (R²=0.45) > autumn (R²=0.30). The correlation between δ¹⁸O and elevation in Jinghe River is low due to the small difference in altitude and short process. The hydrogen and oxygen isotopes of Bortala River and Jinghe River were correlated with chloride, BOD₅ and so on. The correlation coefficients (R) was higher than 0.75 in summer and autumn.