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Diatom assemblages from the diatomaceous deposits of Fayoum depression, Egypt, were analysed to reconstruct the palaeoenvironmental changes during the early to middle Holocene. A total of 283 diatom species and varieties representing 57 genera were identified. The stratigraphic distribution patterns of the recorded diatoms explained eight diatom assemblage zones, which revealed an interesting history of shifts in paleosalinity, pH and water level of the old Fayoum Lake as the water body filled in. Planktonic and benthic-epiphytic assemblages alternate throughout the studied sections. The alternations reflect paleolimnologic conditions as water levels rose and fell. The diatom results have shown four high stands of the freshwater lake level during humid, warmer-wet climatic phases, coinciding with abundance of planktonic Stephanodiscus spp., and Aulacoseira granulata assemblage zones. Rising lake levels are alternated with phases of lowering freshwater lake level with relatively slight rises in salinity and alkalinity. One phase during arid conditions is represented by an abundance of a benthic Navicula radiosa assemblage zone. The second phase during cold and drier climate is dominated by a Staurosira - Staurosirella spp. assemblage zone. The third phase is distinguished by predominance of epiphytic Epithemia spp., Encyonema - Cymbella spp., Synedra spp., and Cocconeis placentula assemblage zones during warm arid conditions. (C) 2014 Elsevier Ltd and INQUA. All rights reserved.