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Polar lakes harbour a unique biogeochemistry that reflects the implications of climatic fluctuations against a susceptible yet extreme environment. In addition to polar, Store Saltsø (Kangerlussuaq, southwestern Greenland) is an endorheic lake with alkaline and oligotrophic waters that host a distinctive ecology adapted to live in such particular physico-chemical and environmental conditions. By exploring the sedimentary record of Store Saltsø at a molecular and compound-specific isotopic level, we were able to understand its ecology and biogeochemical evolution upon climate change. We employed lipid biomarkers to identify biological sources and metabolic traits in different environmental samples (shore terrace, sediment core, and white precipitates at the shore), and their succession over time to reconstruct the lake paleobiology. Different molecular ratios and geochemical proxies provided further insights toward the evolution of environmental conditions in the frame of the deglaciation history of Kangerlussuaq. The relative abundance of terrestrial (i.e., plant derived) biomarkers (odd long-chain n-alkanes, even long-chain n-alkanols, and phytosterols) in the upper half of the shore terrace versus the relatively more present aquatic biomarkers (botryococcenes and long-chain alkenones) in its lower half revealed higher lake water levels in the past. Moreover, the virtual absence of organics in the deepest section of the sediment core (32-29 cm depth) suggested that the lake did not yet exist at the northwestern shore of Store Saltsø ∼5100 years ago. According to the relative abundance of lipid biomarkers detected in the adjacent section above (29-25 cm depth), we hypothesize that the northwestern shore of Store Saltsø formed ∼4900 years ago. By combining the molecular and compound-specific isotopic analysis of lipids in a ∼360 cm sedimentary sequence, we recreated the paleobiology and evolution of an extreme lacustrine environment suitable for the study of the limits of life and the effects of climate warming., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)