Total organic carbon (TOC) content in lake sediments is typically used for the reconstruction of paleoenvironments. It remains uncertain, however, whether these sediment variables in lakes supplied by groundwater in the hinterland of the Badain Jaran Desert are applicable. Moreover, it is still uncertain whether the TOC content in these lakes can be used as a proxy to identify past climatic change and environmental evolution studies. In this study, the spatial distributions of the TOC contents and C/N ratios were analyzed for 109 surface sediment samples collected from five lakes without runoff recharge. The results revealed that the TOC content of the lake surface sediments was extremely low (0.03% - 1.01%) and consisted of both allochthonous organic matter carried by wind, as well as autochthonous organic matter generated in the lakes. Within a lake, spatial differences in the amount of TOC found in surface sediments may be caused by several processes including bathymetry topography and wind-induced wave activity. In addition, wind-induced wave activity produces a higher TOC content, which is more pronounced in larger lakes (>0.21 km2) with longer fetches. By contrast, in smaller lakes, organic matter accumulates in the deeper waters, but can be affected by many factors. It is therefore necessary to consider lake area when applying the TOC content of lake sediments for the reconstruction of a paleolake evolution. Furthermore, because the TOC content of lake sediments in hyper-arid regions is extremely low, and the organic matter may have a multiple and varied sources, a single proxy (TOC) cannot be used to reconstruct lake evolution.