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For lakes in desert hinterlands that are not recharged by river runoff, sediment input solely comes from wind transport. While the processes of sediment transport and deposition in these lakes differ significantly from those with river discharge, the spatial distribution of sediment grain size in these groundwater-recharged lakes remains largely unknown. Moreover, whether the grain size distribution in these lake sediments can be used as a proxy in the study of past climatic change and environmental evolution studies is unclear. In this study, five lakes with a range of surface areas that had no runoff recharge were selected from the hinterland of the Badain Jaran Desert of north-western China, and a total of 108 samples of lake surface sediments were collected to examine the spatial distribution of grain size. Moreover, an end-member-modeling algorithm was used to calculate end members from all grain size measurements. Our results showed that both the median and mean grain sizes in the lake sediments decreased from the nearshore to the offshore, deep-water zone. However, the lowest median and mean grain sizes were not found in the center of the lakes, in contrast to lakes recharged by surface runoff. The median grain size of sediment in the lake center was negatively correlated with lake level, and thus could help reveal lake evolution at low resolutions. Moreover, EM1 and EM2 were interpreted as wind transported sediment, and sediment perturbed by lake waves after wind transport, respectively. The modal grain size of EM1 varied slightly between lakes, while changes in the modal grain size of EM2 were related to lake area. Given the positive relationship found between EM2 content and lake level, changes in the EM2 content (%) can serve as a rough indicator of lake level fluctuations at low temporal resolutions. Copyright (c) 2017 John Wiley & Sons, Ltd.