Mountainous ecosystems are very sensitive towards changes in moisture and temperature and therefore most likely to be affected by climate change. To be able to get a closer insight into the alpine system of the Pamir Mountains, a 1125 cm long core was retrieved from the eastern basin of Lake Karakul (3929 m asl, 12 m water depth), Tajikistan, in 2012. The brackish lake is located in a tectonic basin and the catchment comprises of high alpine steppe to desert with partially snow-covered mountain peaks, up to 6000 m asl, which are the main source of lake water input. Annual precipitation averages at 82 mm and temperatures are around -3.8 °C in the annual mean. To investigate the lacustrine depositional environment of the approximately 29 cal kyr BP old sediment core which contains abundant macrophyte remains, we applied a multiproxy approach by analysing organic and inorganic geochemical parameters (e.g. element contents, stable isotopes, XRF data) and grain-size distribution combined with a subsequent endmember modelling. The key depositional processes in three main sections were identified by analysing the laboratory data. The first reaching from 29 to 16 cal kyr BP is characterized by a low TOC content and high counts of typical indicators for clastic input such as AL2O3 and TiO2. Stable isotopes from authigenic carbonates range from 4.5‰ to 2‰ for δ13C and -0.3‰ to -6‰ for δ18O, reaching a minimum at 21 cal kyr BP. Section two is distinguished by slight increases in TOC and TOC/TN, as well as enrichment in the stable isotopes, whereas the clastic input decreases slowly from 16 to 12 cal kyr BP. The third section displays high TOC and TOC/TN values from 12 cal kyr BP to present and stable isotope values reach their maximum from 10 to 7 cal kyr BP, characterising sub sections within, before following a decreasing trend until present. Indicators of inorganic clastic input reach their lowest values from 8 to 6 cal kyr BP and follow a slight increasing trend afterwards. Our data imply a low biomass productivity during the late Pleistocene with a high external input into the lake basin due to a colder climate and glacial activity. A transition zone characterised by a decrease in external input and a shift towards a higher in-lake productivity follows and indicates climatically induced changes in the sedimentological regime at the transition from the late Pleistocene to the early Holocene. The upper part of the core illustrates a warmer phase since 12 cal kyr BP with reduced influence of glacial activity and a dominance of lake internal signals, revealing high productivity, especially during the last 8 cal kyr BP. Partly high-amplitude changes of the proxies, such as alternating results of stable carbon and oxygen isotopes, which however generally follow the summer insolation (39°N), are presumably induced by short term changes in the environment and surroundings of the lake, yet also major shifts in climate conditions in the region from the late Pleistocene until present are well preserved in the lake record.