The inorganic geochemistry of sediments from El’gygytgyn Lake shift in phase with interpreted paleoclimatic fluctuations seen in the record over the past 250 ka. Warm periods, when the lake was seasonally ice free and fully mixed, are characterized by increased concentrations of SiO2, CaO, Na2O, K2O, and Rb, by decreased contents of TiO2, Fe2O3, Al2O3, and MgO, and by a lower chemical index of alteration (CIA). Increased levels of SiO2 reflect increases in limnic productivity whereas many of the other elements and the CIA likely reflect increased hydrological activity coincident with an increase in coarser sand and silt content and a decrease in clay mineral content. For cold/cooler periods when perennial lake ice cover lead to a stratifed water column and anoxic bottom waters, the opposite is generally observed suggesting a decrease in hydrological activity and an increase in postdepositional chemical alteration. Peaks in P2O3 and MnO, coincident with an increased abundance of vivianite, suggest possible linkages to the paleoproductivity of local fish fauna regardless of climate change across the region surrounding Lake El’gygytgyn. Strontium is high in concentration during warmer intervals and may also be linked to paleoproductivity. Enrichment of the post-Eemian portion of the sediment record in niobium, and yttrium appears independent of glacial–interglacial change; rather it may reflect a gradual shift in the geomorphology of the catchment, particularly the hydrology of large alluvial fans along the western side of the lake. In contrast to some lake records, changes in Zr concentration over time suggests only a weak, if any, increase in eolian sediment supply during colder periods.