This article describes the lake basins of the Jom-Bolok volcanic region in the East Sayan(the largest manifestation of the Holocene eruptions in Central Asia). The geomorphological position, origins, aspects of the structure and development are reviewed considering its sedimentary filling. The limnic morphogenesis here develops under the conditions of contrasting relief, high energy of neotectonic and exogenous processes. We established that Lake Khara-Nur, formed as a result of lava-damming of the Jom-Bolok river valley, emerged in its present form approximately 6500 years ago. A complex record on the environment and climatic changes, acquired from its sediments, made it possible to determine for the first time in this region the long-term trends in the development of the Middle and Late Holocene mountain geosystems and also the distinction of several paleogeographic stages of the formation of the natural environment. An average geochemical record resolution for the bottom sediments of the lake was made uniquely for the East Siberian lake records and is equal to 35 years, while the palynological record approximates 110 years.