Lake El'gygytgyn is situated in a 3.6 Ma old impact crater in northeastern Siberia. Presented here is a reconstruction of the Quaternary lake-level history as derived from sediment cores from the southern lake shelf. There, a cliff-like bench 10 m below the modern water level has been investigated. Deep-water sediments on the shelf indicate high lake levels during a warm Mid-Pleistocene period. One period with low lake level prior to Marine Oxygen Isotope Stage (MIS) 3 has been identified, followed by a period of high lake level (10 m above present). In the course of MIS 2 the lake level dropped to −10 m. At the end of MIS 2 the bench was formed and coarse beach sedimentation occurred. Subsequently, the lake level rose rapidly to the Holocene level. Changes in water level are likely linked to climate variability. During relatively temperate periods the lake becomes free of ice in summer. Strong wave actions transport sediment parallel to the coast and towards the outlet, where the material tends to accumulate, resulting in lake level rise. During cold periods the perennial lake ice cover hampers any wave activity and pebble-transport, keeping the outlet open and causing the lake level to drop.