Mountain lakes in East Siberia have been studied for recent changes in water chemistry, turbidity and diatom assemblages preserved in bottom sediments. We performed a regional analysis of the relative effect of climate and glacier changes on change in diatom diversity and supply of meltware in proglacial lakes. We analysed sediment records from East Siberian glacier lakes using geochemical and diatoms proxies. We found that dramatic changes in communities and abundance of diatoms and biogenic proxy could be induced by low nutrient concentrations in glacial lakes and high turbidity due to active degradation of glaciers and snow patches as a result of the global increase in temperature in the Northern Hemisphere. Our evidences show that diatoms have been gradually decreased since ca. the 1880s. A significant tendency towards diatom reducing occurred at high summer regional temperatures. This tendency may be attributed to the fact that glaciers and snow patches thawed actively in East Siberia during ca. 1880–1958, which was induced by the beginning of the Recent Warming (ca. 1850–1860) and a long period of relatively warm regional climate from ca. 1900 to 1960.