The relationships between thermokarst activity, limnogeological processes and climate change in the Siberian Arctic are not well understood. The objective of this paper is to identify the factors controlling the patterns of deposition, using grain-size distributions, organic contents, elemental compositions and mineralogical compositions of a 137-cm-long sediment core with a maximum age of ~10.9 cal. kyr BP from Lake El’gene-Kyuele, in the tundra of north-eastern Siberia. Eight fine sand layers are attributed to depositional events associated with thaw slump activity acting upon orthogonally oriented patterns of the ice-wedge networks in the ice-rich permafrost on the NW margin of the lake catchment. Sr/Rb ratios, which correspond to the total feldspar and illite content, serve as high-resolution grain-size proxies. The Br content relates to the total organic carbon (TOC) content, and the Fe/Mn ratio reflects the degree of oxidisation. Our results indicate a relationship between repeated phases of fine sand input and retrogressive thaw slumping dependent on hydroclimate variability and orthogonally oriented ice-wedge networks within the catchment.