A combined analysis of magnetic susceptibility, total organic carbon (TOC), biogenic silica (opal), and TiO2 content of the 12.6 m long composite core PG1351 recovered from Lake El’gygytgyn, Chukotka Peninsula, indicate a clear response of the lacustrine sedimentary record to climate variations. The impact is not direct, but through variations in oxygenation of the bottom waters. Mixing of the water body is typical for warmer climates, whereas the development of a stratified water body associated with anoxic conditions at the lake floor appears during cold climates. Oxic conditions lead to a good magnetite preservation and thus to high magnetic susceptibilities, but also to a large-scale degradation of organic matter, as reflected by low TOC (total organic carbon) values. During anoxic conditions, magnetite is severely dissolved yielding very low susceptibility values, whereas organic matter is best preserved, reflected by high TOC values. Hence, in general, neither susceptibility reflects the lithogenic fraction, nor does TOC reflect bioproductivity in case of the studied El’gygytgyn sediments. Based on available infrared stimulated luminescence (IRSL) dating, the obtained susceptibility pattern of core PG1351 shows an obvious correlation to northern hemisphere insolation variations, with a dominating impact of the Earth’s 18 and 23 kyr precessional cycles for the upper half of PG1351, that is, during the past 150 ka. Therefore, the whole susceptibility record, together with biogenic silica (as a proxy for bioproductivity), TOC (as an indicator for redox conditions), and TiO2 (as a proxy for lithogenic input), was systematically tuned to the northern hemisphere insolation yielding an age of about 250 ka for the base of the composite core.