In northeastern Siberia, Russia, a 1.2. m sediment core was retrieved and radiocarbon dated from a small and shallow lake located at the western side of the lower Lena River (N 69°24', E 123°50', 81. m. a.s.l.). The objective of this paper is to reconstruct the palaeoenvironmental variability and to infer major palaeoclimate trends that have occurred since ~. 13.3. cal. kyr BP. We analysed the diatom assemblages, sedimentology (grain-size, total organic carbon (TOC), total nitrogen (TN)), and the elemental and mineralogical composition using X-ray fluorescence (XRF) and X-ray diffractometry (XRD) of the sediment core. Our results show parallel changes in the diatom species composition and sediment characteristics. Enhanced minerogenic sediment input and the occurrence of pyrite is indicative of a cold period between ~. 12.7 and 11.6. cal. kyr BP. The diatom data enable a qualitative inference about the local ecological conditions to be made, and reveal an oligotrophic lake system with alkaline and cold conditions during the earliest Holocene. Moderately warmer climates are inferred for the period from ~. 9.1 to 5.7. cal. kyr BP. The major shift in the diatom assemblage, from dominance of small benthic fragilarioid taxa to a more complex diatom flora with an influx of several achnanthoid and naviculoid diatom species, occurred after a transitional period of about 1400. yr (7.1 to 5.7. cal. kyr BP) at ~. 5.7. cal. kyr BP, indicating a circumneutral and warmer hydrological regime during the Holocene thermal maximum (HTM). Diatom valve concentrations declined starting ~. 2.8. cal. kyr BP, but have been rising again since ≤. 600. cal. yr BP. This has occurred in parallel to the increased presence of acidophilous diatom taxa (e.g. . Eunotia spp.) and decreased presence of small benthic fragilarioid species in the most recent sediments, which is interpreted as the result of neoglacial cooling and subsequent recent climate warming. Our findings are compared to other lake-inferred climate reconstructions along the Lena River. We conclude that the timing and spatial variability of the HTM in the lower Lena River area reveal a temporal delay from north to south. © 2012 Elsevier B.V.