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Abstract The Central Asian Pamir Mountains (Pamirs) are a high‐altitude region sensitive to climatic change, with only few paleoclimatic records available. To examine the glacial‐interglacial hydrological changes in the region, we analyzed the geochemical parameters of a 31‐kyr record from Lake Karakul and performed a set of experiments with climate models to interpret the results. δD values of terrestrial biomarkers showed insolation‐driven trends reflecting major shifts of water vapor sources. For aquatic biomarkers, positive δD shifts driven by changes in precipitation seasonality were observed at ca. 31–30, 28–26, and 17–14 kyr BP. Multiproxy paleoecological data and modelling results suggest that increased water availability, induced by decreased summer evaporation, triggered higher lake levels during those episodes, possibly synchronous to northern hemispheric rapid climate events. We conclude that seasonal changes in precipitation‐evaporation balance significantly influenced the hydrological state of a large waterbody such as Lake Karakul, while annual precipitation amount and inflows remained fairly constant. , Plain Language Summary Lakes in arid Central Asia are particularly susceptible to the rise and fall of lake levels as a consequence of climatic changes. To evaluate drivers behind this phenomenon, we developed a record of humidity and lake levels throughout the last 31,000 years from a high‐altitude lake in the Pamir Mountains. Herefore, we combined hydrological and ecological reconstructions with climate model experiments. Results show that neither the enhanced inflow by melting glaciers nor the significantly increased precipitation amount was responsible for higher lake levels during the studied interval. Instead, reduced summer evaporation during cold episodes was the major trigger for lake transgressions. These fluctuations were driven by changes in radiative forcing (i.e., insolation and hence temperature change) as a consequence of changes in the Earth's orbit around the Sun. As such, our results suggest that a significant impact on lake levels in arid regions is also to be expected by the current anthropogenically driven global warming. , Key Points Proxies for hydroclimate and catchment ecology show insolation‐driven trends, with higher δD values during the LGM similar to outputs from climate models Reduced summer evaporation during cold episodes increased water availability Increased summer moisture caused higher lake levels at 31–30, 28–26, and 17–14 kyr BP coinciding with northern hemispheric rapid climate events