Investigation of the sedimentary record of pre-Alpine Lake Mondsee (Upper Austria) focused on the environmental reaction to rapid Lateglacial climatic changes. Results of this study reveal complex proxy responses that are variable in time and influenced by the long-term evolution of the lake and its catchment. A new field sampling approach facilitated continuous and precisely controlled parallel sampling at decadal to sub-annual resolution for µ-XRF element scanning, carbon geochemistry, stable isotope measurements on ostracods, pollen analyses and large-scale thin sections for microfacies analysis. The Holocene chronology is established through microscopic varve counting and supported by accelerator mass spectrometry 14C dating of terrestrial plant macrofossils, whereas the Lateglacial age model is based on δ18O wiggle matching with the Greenland NGRIP record, using the GICC05 chronology. Microfacies analysis enables the detection of subtle sedimentological changes, proving that depositional processes even in rather large lake systems are highly sensitive to climate forcing. Comparing periods of major warming at the onset of the Lateglacial and Holocene and of major cooling at the onset of the Younger Dryas reveals differences in proxy responses, reflecting threshold effects and ecosystem inertia. Temperature increase, vegetation recovery, decrease of detrital flux and intensification of biochemical calcite precipitation at the onset of the Holocene took place with only decadal leads and lags over a ca. 100 a period, whereas the spread of woodlands and the reduction of detrital flux lagged the warming at the onset of the Lateglacial Interstadial by ca. 500–750 a. Cooling at the onset of the Younger Dryas is reflected by the simultaneous reaction of δ18O and vegetation, but sedimentological changes (reduction of endogenic calcite content, increase in detrital flux) were delayed by about 150–300 a. Three short-term Lateglacial cold intervals, corresponding to Greenland isotope substages GI-1d, GI-1c2 and GI-1b, also show complex proxy responses that vary in time. Copyright © 2011 John Wiley & Sons, Ltd.