[1] Lake Moeris lends its name to the extinct proboscidean mammal Moeritherium, a distant relative of modern elephants first described from the nearby Qasr el Sagha Formation.

During the Messinian Salinity Crisis of the late Miocene, the Nile flowed past the empty Faiyum basin at the bottom of a large canyon which reached some 2.4 kilometres (1.5 mi) deep where the city of Cairo now sits.

[2] Stone flakes found along the margins of the Faiyum basin matching those produced by the Levallois technique suggest that the shores of Lake Moeris were inhabited by humans as far back as the Middle Paleolithic.

[2][13] Other archaeological work in the Faiyum basin, particularly that of Gertrude Caton-Thompson and Elinor Wight Gardner, has recovered evidence of numerous Epipaleolithic and Neolithic settlements.

The first major manmade alterations to Lake Moeris occurred during the Middle Kingdom under the kings of the Twelfth Dynasty, who ruled from the Faiyum region following the move to the new royal capital of Itjtawy.

With this new governance and the concurrent influx of Greek and Macedonian colonists into Egypt, the Faiyum basin and Lake Moeris was developed further to enhance its capacity as an agricultural center.

The royal engineers of Ptolemy II Philadelphus constructed additional canals and levees, as well as a dam on the Bahr Yussef to regulate the inflow of the Nile, allowing for further settlement of the basin and increased grain production as the lake's waters receded and exposed new fertile soils.

[3][4] Numerous papyri recovered from Ptolemaic-era sites in the Faiyum (often from waste papyrus used for cartonnage) preserve correspondence between engineers and administrators during this period of development, including the archive of Zenon of Kaunos.

By the end of the Ptolemaic Kingdom, routine maintenance of this irrigation system had been neglected due to internal strife, causing croplands within the Faiyum to either dry up or become totally inundated.

The revitalization of agriculture within the Faiyum was met with another wave of settlement and the area saw sustained productivity until the Crisis of the Third Century, when another civil war destabilized the region and the irrigation system once again fell into disrepair.