Past and present climate changes on the earth’s northern hemisphere were amplified particularly in Arctic and Subarctic regions because of feedbacks related to sea-ice distribution, intensity of soil carbon release and changes in the freshwater balance. Palaeoenvironmental changes in these realms are known to be spatio-temporal highly variable. Lake sediments from periglacial regions represent important archives of past environmental changes related to direct and indirect climate influences as well as local limnogeological processes. As compared to other high latitude regions, knowledge gaps still exist in the remote and vast areas of NE Siberia, Russia. The aim of this work is to contribute to a better understanding of the Holocene environmental variability in this area, taking into account local dynamics of thermokarst processes and their influence on the depositional environments of lakes. The thesis comprises three research articles on radiocarbon-dated sediment cores from three lakes in northern Yakutia. The lakes are located at the western side of the lower Lena River. Lake Sysy-Kyuele belongs to the subarctic forest-tundra zone. Lake El’gene-Kyuele is located in the arctic tundra near the Lena-Olenek watershed. Another tundra lake, informally called “Lake 09-Tik-03”, is part of the western Lena River Delta. The distributions of multiple indicators of past conditions were analysed along the sediment cores including (1) species distributions of siliceous microalgae (diatoms), (2) grain size distributions (laser particle sizing), (3) element (XRF) and (4) mineral (XRD) compositions as well as (5) the carbon and nitrogen (CNS, TOC) contents. The analyses of the sediment core from Lake Sysy-Kyuele (121 cm) show that small benthic fragilarioid taxa were dominant since ~12.7 cal. kyr BP. Influx of several benthic achnanthoid and naviculoid species started gradually between ~7.1 and 5.7 cal. kyr BP, parallel to increasing diatom valve concentrations (DVC). DVC declined at ~2.8 cal. kyr BP but started to rise again ≤600 cal. years BP, in parallel to increasing acidophilic Eunotia taxa. The sediment core from “Lake 09-Tik-03” (109 cm) contains predominantly benthic achnanthoid and naviculoid diatom species. Araphid species in this sediment core are represented by peak occurrences of small benthic fragilarioid taxa at ~3.0 cal. kyr BP and Tabellaria flocculosa at ~1.3 cal. kyr BP. Diatoms are not present in the El’gene Kyuele sediment record. Downcore elemental and mineral composition of the sediment cores indicates detrital minerogenic input and authigenic mineral precipitation depending on the local limnogeological and thermokarst setting. The aim of reconstructing the palaeoclimatic variability was achieved mainly from the Sysy-Kyuele lake archive. Past climate variations were inferred from responses of the diatom assemblage and physic-chemical parameters to limnological and environmental changes related to ice-cover, vegetation and soil. The Younger Dryas period correlates with the occurrence of framboidal pyrite, attributed to the formation of anoxic bottom water conditions during prolonged seasonal lake ice cover. The diatom distribution and valve concentrations indicate a Holocene Thermal Maximum (HTM) from ~7.1 to ~2.8 cal. kyr BP followed by Neoglacial cooling and a subtle recent warming. In parallel, the diatom data suggest a long-term acidification trend during natural lake ontogeny. Regional implication of the environmental reconstruction reveals a delay from north to south along the Lena River in the spatio-temporal pattern of the HTM. Delayed warming in this area can be explained by the supply of cold air masses from melting Laurentide ice sheets in the north Atlantic region. In contrast, changes in the diatom assemblages in the sediment core from “Lake 09-Tik-03” were attributed to local thermokarst processes. Permafrost degradation and probably thermokarst-induced water supply influenced the aquatic ecosystem ~1.3 kyr BP via changes in habitat availability, hydrochemistry, and lake level. Analyses of the sediment core from Lake El’gene-Kyuele (137 cm) reveal that permafrost degradational processes at the NW lake margin resulted in pulses of coarse detrital input from nearby slopes. The cyclic sedimentary events probably reflect both precipitation variability and the patterned structure of the ice-rich permafrost catchment. The orthogonal ice-wedge system, oriented parallel to the shoreline, may cause cyclic intensification (outcropping polygons) and reduction (outcropping ice wedges) of retrogressive thaw slumping, rather than temperature-driven mechanisms. In conclusion, the multiproxy study of the sediment core from the forest-tundra lake Sysy-Kyuele improves the knowledge of the palaeoclimate variability in NE Siberia. Hence, further studies of sediment archives with higher temporal resolution from comparable lake systems in the closer area are promising. The analysis of the sediment cores from the tundra lakes provides new insights into thermokarst-driven limnogeological processes that, however, depend on local permafrost settings. These works clearly indicate that palaeoecological research in NE Russia would greatly benefit from further freshwater diatom studies.