Abstract: The lakes, located in the southeast of the Badain Jaran Desert, are one of most significant water resources in this desert. In order to reveal the potential recharge sources and recharge modes of lakes and explore the spatial variation characteristics of chemical ions and influence factors on lake water, the stable isotopic (δ18O and δD) characteristics and hydrochemical features of lake water in the Badain Jaran Desert had been systematically analyzed. The results were as follows: the average values of pH and Ec for lake water were 9.29 and 291 mS/cm respectively, and the main ions of lake water were Na+ and Cl-, accounting for 69.4% of total ions. The average values of δ18O and δD for lake water were 6.42‰ and -3.67‰ respectively. The evaporation effects on lakes in different regions varied significantly, and the evaporation intensity of lakes gradually increased from the southeastern to the northwestern of this desert. Based on the isotope-elevation relationship equation, the potential recharge source of lakes was the atmospheric precipitation from the Yabulai Mountains located in the southeast of this desert, and the recharge mode of lakes was mainly the lateral recharge from the surrounding groundwater. The recharge sources and regional rock weathering were the main controlling factors for the spatial variation of lake water ions in this desert.