High-altitude ecosystems react sensitively to hydroclimatic triggers. Here we evaluated the ecological and hydrological changes in a glacier-influenced lake (Hala Hu, China) since the last glacial. Rapid fluctuations of aquatic biomarker concentrations, ratios, and hydrogen isotope values, from 15 to 14,000 and 8 to 5000 years before present, provided evidence for aquatic regime shifts and changes in lake hydrology. In contrast, most negative hydrogen isotope values of terrestrial biomarkers were observed between 9 and 7,000 years before present. This shows that shifts of vapour sources and increased precipitation amounts were not relevant drivers behind ecosystem changes in the studied lake. Instead, receding glaciers and increased meltwater discharge, driven by higher temperatures, caused the pronounced ecological responses. The shifts within phytoplankton communities in the Late Glacial and mid Holocene illustrate the vulnerability of comparable ecosystems to climatic and hydrological changes. This is relevant to assess future ecological responses to global warming.