This paper is the result of environmental geological survey engineering. 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 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 (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. Conclusions 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. The lakes in desert are highly sensitive to climate change. The changes of salt mineral assemblage and content in desert lakes can be used as an important basis for discussing environmental problems such as global warming and desertification.