The origin of the vast amount of water of the Nubian aquifer system in northeast Africa has been under controversial discussion among hydrogeologists. Does the water flow under more or less steady state conditions from intake beds in the humid Tibesti mountains or in the Ennedi mountains in Chad? Or was it recharged locally in the vicinity of the present oases during an earlier more humid climate so that present extraction actually means groundwater mining under unsteady conditions? An answer from a hydrodynamic point of view is presented using a two-dimensional horizontal finite element groundwater model simulating large-scale flow from the Chad to the Qattara depression. It includes a leakage concept for the confined northern part in order to simulate possible recharge in the vicinity of the east Saharian depressions during humid phases. According to steady state simulations, infiltration solely in the southern highlands does not suffice to maintain the presently observed water levels. Large-scale flow from the Chad highlands to the Qattara depression is insignificant. Thus the system was mainly filled by local recharge. A calibration for the 1960–1980 period was carried out on the model in order to adjust geological system parameters in the vicinity of the Egyptian depressions. An 80 years simulation for the future extraction of planned pumping centres in Egypt and Libya leads to the conclusion that there will be little interference between them in the unconfined part but a common drawdown cone in the Egyptian New Valley area. Some water extracted in Egypt will be drawn from Sudan and Libya. The existing projects in Egypt and Libya extract about 0.5 km3year−1, being the same order of magnitude as the natural groundwater discharge. The combined future projects would extract 5 km3year−1, which is about ten times the natural outflow. Thus these projects would change the natural groundwater flow system completely. A comprehensive explanation of the aquifer behaviour seems to indicate a groundwater age far beyond the apparent14C ages. Groundwater mainly flows between regions of (former) recharge and discharge. The presently extracted groundwater of the Egyptian oases was formed to a great extent during several humid phases in the unconfined part of the Nubian Aquifer in south-west Egypt. This part of the aquifer has been in a depleting process for several thousand years.