Quaternary limnic sediments from Velanska Cesta, a former lake in the Czech Republic, were investigated to document the response of an aquatic environment to global climatic shifts during the late Pleistocene-early Holocene transition. The obtained multi-proxy record, including subfossil diatoms, diatom-inferred variables (index of trophic state, halobic index, TP, and pH), plant macrofossils, and geochemical data, was compared with the delta O-18 GISP2 curve. Diatom accumulation zones and subzones established on the basis of a ConSLink cluster analysis corresponded well with the boundaries of the Bolling, Older Dryas, Allerod, Younger Dryas, and Preboreal periods. The diatom-inferred trophic state and salinity data showed increased values during the colder epochs, which were supported by the findings of low-temperature macrofossil indicators in the corresponding samples. The results of this study document a long-term forcing of a shallow lacustrine ecosystem in central Europe by climatic events of a global scale.