Long (multi-millennial), continuous lake pollen records have provided insights into terrestrial ecosystem responses to orbital- and sub-orbital-scale climate forcing. By comparison, the potential of diatoms and stable isotopes to provide additional insights into limnetic response over comparable timescales has not been explored to the same extent, particularly in the Mediterranean region, even though such proxies are known to respond sensitively and rapidly to environmental change. Here we present a 19,000-year multiproxy record of limnetic change in the Ioannina basin, NW Greece, spanning the penultimate interglacial–glacial transition and the early penultimate glacial (c. 189–170 ka BP). The diatom record, the first from this interval in Southern Europe, reveals that lake conditions changed in concert with muted millennial-scale climate oscillations thought to originate in the North Atlantic, demonstrating clearly the sensitivity of diatoms to sub-orbital climate variability. Diatom and isotope-inferred changes in lake conditions coincided with the MIS 7/6 transition, whilst the new δ18O record suggests increased moisture availability in SE Europe during MIS 6.5, adding support for a Mediterranean-wide increase in precipitation. Comparison with pollen data from the same sequence demonstrates that lake and terrestrial ecosystems co-varied, with no delay in forest expansion in response to climate change during this interval. Substantial changes in lake conditions contrast with subdued changes in catchment vegetation during an 8000 year-long cold interval in the early penultimate glacial. This may reflect differences in limnetic and terrestrial thresholds of response to environmental change, and perhaps also the influence of site specific factors in modulating terrestrial ecosystem response.