We have compared δ18O and δ13C compositions of ostracod valves with elemental and grain size records of bottom sediments from the drill core KDP-01 (Northern Mongolia, NM) formed for the last 330 ka BP. The increase in the δ18O values, a high content of Br, and a low percentage of clay particles were found to positively correspond with high lake bio-productivity and “warm” marine isotope stages (MIS-3, 5, 7, and 9) and visa versa during “cold” MIS-stages. Positive δ13C values have been linked with high inflowing dissolved inorganic carbonates, and forest-steppe vegetation seems to be evidenced during “cold” MIS stages (MIS-2, 4, 6, and 8). Sharp depletions in the δ18O values on 1.5–2.5 ‰ occurring during the ends of MIS-6 and MIS-4 could be induced by glacier meltwater discharge into Lake Khubsugul. However, shifts in the δ18O values were not significant in MIS-2 and MIS-8, based on our assumption that the inflow rates of glacier meltwater were low due to the relatively small sizes of glaciers in the NM during these stages. During MIS-2, Northern Mongolian glaciers were the smallest in sizes due to high regional aridity. The climate condition in MIS-3 was not typically favorable for a “warm” MIS-stage, while glaciers or snow patches formed in MIS-4 most likely were still in the NM. As a result, isotopically depleted δ18O meltwater was supplied into Lake Khubsugul at the period.