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Anthropogenically-driven climate warming and land use change are the main causes of an ongoing decrease in global biodiversity. It is unclear how ecosystems, particularly freshwater habitats, will respond to such continuous and potentially intensifying disruptions. Here we analyse how different components of terrestrial and aquatic ecosystems responded to natural climate change during the Lateglacial. By applying a range of analytical techniques (sedimentology, palaeoecology, geochemistry) to the well-dated sediment archive from Lake Hämelsee (Germany), we show evidence for vegetation development, landscape dynamics and aquatic ecosystem change typical for northwest Europe during the Lateglacial. By particularly focussing on periods of abrupt climate change, we determine the timing and duration of changes in biodiversity in response to external forcing. We show that onsets of changes in biodiversity indicators (e.g. diatom composition, Pediastrum concentrations) lag changes in environmental records (e.g. loss-on-ignition) by a few decades, particularly at the Allerød/Younger Dryas transition. Most biodiversity indicators showed transition times of 10–50 years, whereas environmental records typically showed a 50–100 year long transition. In some cases, transition times observed for the compositional turnover or productivity records were up to 185 years, which could have been the result of the combined effects of direct (e.g. climate) and indirect (e.g. lake stratification) drivers of ecosystem change. Our results show differences in timing and duration of biodiversity responses to external disturbances, suggesting that a multi-decadal view needs to be taken when designing effective conservation management of freshwater ecosystems under current global warming. • Multi-proxy approach applied to Lateglacial sediment record from Germany. • Detailed palaeoenvironmental and palaeoclimatic reconstruction. • Decadal-scale lags in biodiversity responses to climate change. • Ecological transitions to a new stable state typically take 10–50 years. [ABSTRACT FROM AUTHOR]