The Sahara Desert, known today as one of the world's great wildernesses, was periodically dotted with large lakes that formed during the Holocene pluvial periods. As the lakes dried, the fertile and flat‐lying damp muds formed a rich habitat that was occupied by human settlers before being abandoned, as the area dried out completely. In Kharga, our work shows that a combination of pluvial periods with short term storage in the Upper Nubian aquifer, access to artesian water in the Lower Nubian Aquifer and over‐flow water from the Nile via the Wadi Toshka created a biodiverse environment which, although drier today, sustained refugia of plants and animals throughout the Holocene.