Occupation of the Egyptian Western Desert during the Holocene is linked with the summer monsoon, the position and intensity of the Inter-Tropical Convergence Zone (ITCZ) and the use of internal lakes and playas fed by summer rain. In contrast, such correlations are absent for the Fayum region of Egypt where occupation instead correlates with mid-Holocene increases in intensity of Mediterranean winter rainfall. Lake Qarun in the Fayum was the only lake where Near Eastern plant domesticates were used during the early-mid-Holocene period. Analysis of radiocarbon determinations is presented which suggests that, unlike later agriculture in the Nile Valley, early use of domesticates in the Fayum involved a dependence on winter rains for cereal cultivation following the Mediterranean growth seasons. It is proposed that the switch to a winter growing season after summer inundation occurred later, probably as part of key socio-economic changes during the Egyptian Predynastic period.