A new dataset from Lake Emanda provides insights into climate and environmental dynamics in an extreme continental setting in northeastern Siberia. The δ18Odiatom record is supported by diatom assemblage analysis, modern isotope hydrology and atmospheric circulation patterns. The data reveal a relatively cold oligotrophic freshwater lake system persisting for the last ∼13.2 cal ka BP. Most recent δ18Odiatom (+21.5‰) combined with present-day average δ18Olake (−16.5‰) allows calculating Tlake (∼21 °C), reflecting summer conditions. Nonetheless, the δ18Odiatom variability is associated with changes in δ18Olake rather than with Tlake. An obvious shift of ∼2‰ in the δ18Odiatom record at 11.7–11.5 cal ka BP accompanied by significant changes in diatom assemblages reflects the onset of the Holocene. Relatively high δ18Odiatom during the Early Holocene suggests relatively warm and/or dry climate with associated evaporation effects. The absolute maximum in δ18Odiatom of +27.7‰ consistent with high values of diatom indices at ∼7.9–7.0 cal ka BP suggests a Mid Holocene Thermal Maximum. A continuous depletion in δ18Odiatom since ∼5.0 cal ka BP is interpreted as Middle to Late Holocene cooling reaching the absolute minimum at 0.4 cal ka BP (i.e. the Little Ice Age). An overall cooling trend (∼0.3‰ 1000 yr−1) throughout the Holocene follows decreasing solar insolation. The pattern of the Lake Emanda δ18Odiatom record is similar to that obtained from Lake El’gygytgyn suggesting a common “eastern” regional signal in both records, despite their hydrological differences. Presently, atmospheric moisture reaches the study region from the west and east with ∼40% each, as well as ∼20% from the north.