The character and impact of climate change since the last glacial maximum (LGM) in the eastern Mediterranean region remain poorly understood. Here, two new diatom records from the Ioannina basin in northwest Greece are presented alongside a pre-existing record and used to infer past changes in lake level, a proxy for the balance between precipitation and evaporation. Comparison of the three records indicates that lake-level fluctuations were the dominant driver of diatom assemblage composition change, whereas productivity variations had a secondary role. The reconstruction indicates low lake levels during the LGM. Late glacial lake deepening was underway by 15.0 cal kyr BP, implying that the climate was becoming wetter. During the Younger Dryas stadial, a lake-level decline is recorded, indicating arid climatic conditions. Lake Ioannina deepened rapidly in the early Holocene, but long-term lake-level decline commenced around 7.0 cal kyr BP. The pattern of lake-level change is broadly consistent with an existing lake-level reconstruction at Lake Xinias, central Greece. The timing of the apparent change, however, is different, with delayed early Holocene deepening at Xinias. This offset is attributed to uncertainties in the age models, and the position of Xinias in the rain shadow of the Pindus Mountains.