Ostracods possess bivalve carapaces composed of low-Mg calcite, which can be preserved in a variety of sedimentary environments. They are a useful paleoenvironmental indicator, in particular for non-marine environments. Although previous studies of Lake Baikal and Lake Hovsgol have provided some evidence of large-scale paleoenvironmental changes in central Asia during the late Pleistocene, trace element records in ostracods from these two lakes, which may reveal the detailed limnological processes, have not yet been reported. In this study, we analyzed stable isotopes and trace elements in ostracods in three gravity core sediments recovered from Lake Hovsgol, northern Mongolia, to reconstruct the long-term limnological histories of the lake. Radiocarbon dating results indicated that ostracod-bearing core sediments were deposited from ∼14.5 to 21.5 ka, which corresponds to the early stage of the last deglaciation, including the Last Glacial Maximum (LGM). The Mg/Ca and Sr/Ca ratios from two species of ostracods, C. lacustris and L. inopinata, ranged from 4 to 25 and 3–5 mmol/mol, respectively, with distinct and consistent decreasing trends. The changes in the Mg/Ca and Sr/Ca ratios indicate that the salinity of the lake water decreased substantially at the initial transition from the last glacial to the current interglacial period, which was mainly due to the ice melting and introducing fresh water into the lake. Changes in the Fe/Ca and U/Ca ratios were interpreted as water circulation changes in the bottom of the lake. After the LGM, the Fe/Ca and U/Ca ratios gradually increased, indicating that inflowing cold water induced stronger water circulation and subsequently a higher dissolved oxygen content in the bottom water of the lake. The Mn/Ca ratio had the opposite trend to the U/Ca and Fe/Ca ratios, which suggests that it was affected by the weathering intensity in the area around Lake Hovsgol. The stable isotopic results for C. lacustris support our paleoenvironmental interpretations in the region on the basis of trace elements. As a result, ostracod geochemical records from Lake Hovsgol, northern Mongolia, provide new insights into paleoenvironmental changes in central Asia during the onset of the last deglaciation.