The mineral deposit of salt lakes was widely used to reconstruct paleoenvironment. However, whether mineral composition and deposition characteristic in no runoff recharged lakes is different from that in runoff recharged lakes remains uncertain. In this paper, we collected 33 lake surface sediment samples from groundwater recharged lakes with different salinity and 10 surface aeolian sand samples in the Badain Jaran Desert. Mineralogical assemblages of all the samples were measured by X-ray diffraction. Results indicated that lake surface sediments were mainly composed of detrital minerals such as quartz, feldspar, pyroxene and mica. Moreover, some lakes included small amounts of carbonate and chlorine. Saline mineralogical assemblages in lake sediment varied with the lake water salinity:freshwater lake contains only detrital mineral, brackish one contain both detrital mineral and carbonate, and saline ones contain detrital mineral, carbonate and chloride simultaneously. The content of detrital minerals in aeolian sand samples was 90%, which indicated that the aeolian sand had a great contribution to the lake surface sediments mineralogical assemblages, while the saline minerals in lake surface sediments were authigenic minerals. Hence, the composition and distribution of saline minerals could respond to the changes of water salinity, and have same environmental significance compared with that in runoff supply salt lakes. Moreover, lake mineralogical assemblages in the surface sediments of groundwater recharged lakes can be a proxy for paleoclimate and palaeoenivronment reconstructions.