Thermokarst lakes are a wide-spread feature of permafrost affected landscapes, of which highly dynamic geomorphological and environmental processes are closely connected with current and past climate variability. This study investigated Late Quaternary sedimentary dynamics, basin evolution, relative lake level variability, and environmental interrelations of the northern Siberian Lake El'gene-Kyuele (71°17'N, 125°34'E), which contains characteristics of an Arctic Ice Complex thaw-lake and of a Yakutian alas. The study area is characterized by an extreme continental Arctic climate, deep continuous permafrost, a topographically dissected terrain, and a current vegetation of arctic shrub tundra. For reconstruction of past thermokarst processes, the sediment archive PG2038-1 at the modern eastern shore was investigated by field observation, geochronology, sedimentology, biogeochemistry, and the analysis of plant macrofossils and was compared to preceding investigations of nearby archives. The results reveal two main sources for sediments in the lake basin: terrigenous diamicton provided by thermokarst slopes, and lacustrine detritus that has mainly settled in the deep lake basin. Lake El'gene-Kyuele and its adjacent thermokarst basin rapidly expanded during the Early Holocene/Holocene Thermal Maximum. This climatically warmer period was characterized by open woodlands composed of larch, birch trees, and shrubs, which were eventually affected by fire. The maximum lake depth, and the lowest limnic bioproductivity, at the modern eastern shore occurred as the longest period of about 7,000 yr throughout the progressively cooler Neoglaciation. Partial drainage and a westerly lake migration occurred ca. 1,000 cal. yr BP as a non-climate-driven thermokarst process.