Sediment cores from Lake Qarun provide a record of mid-late Holocene climatic changes in Northern and Eastern Africa as well as environmental changes due to the activities of ancient Egyptians. We used sedimentological, mineralogical, and geochemical analyses of the cores to investigate long-term variations in lake level due to changing hydrologic inputs. An age model based on three paired 14C and paleomagnetic measurements suggests that the base of the sediment cores is as old as ∼5000 B.C.E. Geochemical analyses indicated that lake sediments were derived from Nile floods with an admixture of Saharan sand. Laminated endogenic carbonate-rich clayey silt lithofacies with benthic diatoms are indicative of relatively low lake levels, saline waters and dry conditions; massive lithofacies with planktonic diatom species are indicative of relatively high lake levels, fresh waters and humid conditions. Faintly laminated clayey silt lithofacies suggest intermediate conditions. Variations in lithology as well as diatom composition suggest that the lake level has varied from relatively high levels in its early history to lower levels in later years although there have been numerous cycles in water level over the past 7000 years. A combination of climate changes in the source area of the Nile River as a result of monsoon dynamics; climatic changes in the setting area of the Lake Qarun; and human activities through the dynasties in Egypt produced these variations in lake level.