Thermokarst activity is a widespread arctic feature in Arctic periglacial regions. The highly dynamic relationships between limnogeological processes, permafrost degradation/aggradation and climate change, however, are yet not fully understood. To gain insight into the complex nature of climatic and non-climatic processes in the Arctic, we investigated palaeoenvironmental archives in a thermokarst landscape setting at Lake El’gene-Kyuele (71°17'N, 125°34'E, 157 m a.s.l.) in the tundra of northeastern Siberia. The lake is about 3 km long and 0.5 km wide with a maximum water depth of 10.5 m. It is located 125 km southwest of Tiksi near the Lena Delta, on the southern part of the watershed between the Lena and Olenek rivers. The waterbody is cutting into Holocene alas and Pleistocene Ice Complex sediments. In the latter case, thaw slumps occur associated with increased sediment transport. We analysed grain-size distributions, organic matter contents, elemental and mineralogical compositions, stable carbon isotopes, and plant macrofossils in sediment cores from the bottom and the shoreline of the lake. Sr/Rb ratios (related to feldspar and illite) serve as high-resolution grain-size proxies, Br correlates with the TOC content, and the Fe/Mn ratio reflects the degree of oxidisation. Radiocarbon dated samples indicate that the Late Pleistocene was affected by fire, which potentially triggered the initiation of thermokarst processes. A number of fine sand layers with the maximum age of ~10.9 cal. kyr BP is linked to depositional events associated with thaw slump activity on the thermokarst slopes. Besides the general dependence on hydroclimate variability, repeated phases of fine sand input and retrogressive thaw slumping indicate a close linkage with the orthogonally oriented patterns of the ice-wedge networks in the ice-rich permafrost within the catchment area. During the early Holocene Thermal Maximum (HTM) the lake rapidly expanded surrounded by forest or forest tundra vegetation composed of larches, birch trees, and shrubs. Maximum lake depth and lowest limnic bioproductivity occurred during the longest time interval of about ~7 kyr starting in the HTM and lasting throughout the progressively cooler Neoglaciation. Partial drainage and a westerly migration occurred ~0.9 cal. kyr BP. We conclude that the limnogeological regime (within the lake) is driven by small-scale processes depending on the spatial permafrost variability, whereas the lake development as landscape feature was driven by both, the climate history and the local environmental setting.