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This paper reports new multi-proxy palaeoenvironmental data on the late Glacial-Holocene transition (c. 14.8-9.3 ka) in equatorial East Africa, in the form of microfossil assemblages (chironomids, diatoms and ostracods) recovered from the sediment record of Lake Emakat, Empakaai Crater, northern Tanzania. In the context of available palaeoclimatic and palaeoecological information from the region and previously published fossil pollen and carbon and nitrogen isotopic data for the same sediment sequence, we here reconstruct local lake-system response to regional climatic and hydrological instability during the period of post-glacial warming. The aquatic biological proxy indicators suggest that the water level and chemistry of Lake Emakat evolved, first from a shallow freshwater body at 14.8 ka to a deeper freshwater phase between c.14.4 and 10.3 ka and then to a markedly shallower, alkaline-saline environment after c.10.3 ka. The lake appears to have been deepest between 13.2 and 12.0 ka, at a time of climatic drying when moist montane forest vegetation within the lake's crater catchment was being replaced by open wood-and scrubland. Some palaeohydrological changes reconstructed for Lake Emakat are in phase with lake evolution elsewhere in the region and thus apparently track broad-scale climate changes, but some are not. Collectively these multi-proxy paleolimnological data indicate a complex adjustment of the local aquatic ecosystem to temporal variations both in total annual effective precipitation and its seasonal distribution. The lake's hydrological response was further conditioned by local factors, notably its geological and topographic setting.