Lake El'gygytgyn/NE Russia holds a continuous 3.58 Ma sediment record, which is regarded as the most long-lasting climate archive of the terrestrial Arctic. Based on multi-proxy geochemical, mineralogical, and granulometric analyses of surface sediment, inlet stream and bedrock samples, supplemented by statistical methods, major processes influencing the modern sedimentation in the lake were investigated. Grain-size parameters and chemical elements linked to the input of feldspars from acidic bedrock indicate a wind-induced two-cell current system as major driver of sediment transport and accumulation processes in Lake El'gygytgyn. The distribution of mafic rock related elements in the sediment on the lake floor can be traced back to the input of weathering products of basaltic rocks in the catchment. Obvious similarities in the spatial variability of manganese and heavy metals indicate sorption or co-precipitation of these elements with Fe and Mn hydroxides and oxides. But the similar distribution of organic matter and clay contents might also point to a fixation to organic components and clay minerals. An enrichment of mercury in the inlet streams might be indicative of neotectonic activity around the lake. The results of this study add to the fundamental knowledge of the modern lake processes of Lake El'gygytgyn and its lake-catchment interactions, and thus, yield crucial insights for the interpretation of paleo-data from this unique archive.