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Two gravity cores (1.1 and 2.2 m long) of deep-water bottom sediments from Lake Khubsugul (Mongolia) were studied. The Holocene, biogenic silica and organic matter-rich part of the first core was subjected to AMS radiocarbon dating which placed the date of dramatic increase of pelagic diatoms (40 cm below sediment surface) at a calendar age of 11.5 cal ky BP. ICP-MS analysis of weak nitric acid extracts revealed that the upper Pleistocene, compared to the Holocene samples, were enriched in Ca, C
inorg, Sr, Mg and depleted of U, W, Sb, V and some other elements. Transition to the Holocene resulted in an increase of total diatoms from 0 to 10
8 g
−1, of BiSi from 1% to 20%, of organic matter from <1% to >6%. The Bølling–Allerød–Younger Dryas–Holocene abrupt climate oscillations manifested themselves in oscillations of geochemical proxies. A remarkable oscillation also occurred at 22 cm (ca. 5.5 ky BP). The Pleistocene section of the second, longer core was enriched in carbonate CO
2 (up to 10%) and water-extractable SO
4
2− (up to 300 times greater than that in Holocene pore waters). All this evidence is in an accord with the earlier finding of drowned paleo-deltas at ca. 170 m below the modern lake surface of the lake [Dokl. Akad. Nauk 382 (2002) 261] and suggests that, due to low (ca. 110 mm) regional precipitation at the end of the Pleistocene, Lake Khubsugul was only 100 m deep, and that its volume was ca. 10 times less than today.