Sedimentary sequences up to 4.71 m thick and up to ~24 ka were made by drilling the bottom sediments in three lakes of the Boguty depression. This is the highest mountain (2390–2470 m a.s.l.) and longest sedimentary record for the neighboring areas of Altai, Tuva, and Mongolia, which reflects the course of natural processes in the highest and most arid part of Russian Altai from the Last Glacial Maximum until the present day. As early as in the first stage of this study, the reservoir effect for moraine-dammed Upper Boguty Lake is estimated at 290 years for the present and 1.2 and 1.3 ka for the boundaries at ~5.7 and ~9.6 ka, respectively. Using a complex of analytical methods, the sedimentological transition zone between the Late Pleistocene glacial–lacustrine clays and the Holocene biogenic–terrigenous silts is identified at 16–13 ka ago; the size of glaciers in MIS-2 and in the Younger Dryas, as well as the time of formation of thermokarst lakes (no later than 8.7 ka), within the upper terminal moraine complex is established. Widespread tree vegetation in the now treeless Boguty depression in the first third of the Holocene is confirmed.