[Objective] It is of great significance to understand the distribution pattern of saline mineral deposits in lake basin for the reconstruction of palaeoenvironment and palaeohydrology. However, the studies on mineral distribution for groundwater recharged lake sediments are few, which hinders the climate-environmental reconstruction in arid area. [Methods]The Badain Jaran Desert, located in western Inner Mongolia in a hyper-arid area of China, is characterized by the coexistence of more than 110 perennial lakes and thousands of mega-dunes. More than 90% of the recharge of lakes between mega-dunes is from groundwater. In this study, we analyzed the mineral assemblage and distribution characteristics of the surface sediments of eight lakes with different salinity in the Badain Jaran Desert. [Results]The results show that: 1) For individual lakes, the distribution pattern of saline mineral deposits is similar to those of lakes with runoff recharge, that is, there are more detrital mineral deposits at the edge of the lake, and the saline mineral deposits gradually increase towards the lake interior, and the mineral types gradually change from carbonate to sulfate and chloride. 2) The mineral composition of the sediments near the lake edge is more easily affected by the variation of lake water level and area, while the sediments near the lake center may be affected by the water depth and the groundwater recharge. 3）The shallow lakes are well mixed and are not easily affected by the stratification of lake salinity and water temperature, and the replenishment of fresh water at the bottom. Moreover, the total content of salt minerals has a good linear relationship with the salinity of lake water. [Conclusion] The changes of saline mineral assemblage and its content in the lakes recharged by groundwater can well reflect the changes of lake salinity and can be used as a proxy of climate-environmental reconstruction in desert areas. This study will provide an important basis for the reconstruction of palaeohydrological information using lake saline deposits in arid areas of China.