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Groundwater is the only water resource across the "hyper" arid Eastern Sahara. Management of this resource is imperative for the sustainable development approaches. A 3D GIS-based groundwater flow model for the Nubian Sandstone Aquifer System (NSAS) was developed to simulate the groundwater management options for the different development areas/oases within the aquifer, and to predict the environmental impact of the present and future groundwater extraction schemes on the whole system. Based on the actual and planned extraction rates of the NSAS, five extraction scenarios were suggested to investigate the most feasible groundwater management option in terms of the economic lifting depth until year 2100. The model was calibrated and validated under the transient conditions. The calibrated model was then used for the prediction simulations. The results of simulating the present extraction rates of the NSAS until 2100 showed that the free flowing phenomenon will disappear all over the modeled area. At this simulation time, a groundwater volume of 354 km(3) will be extracted from the aquifer storage. Scenario 3 was found to be the optimal groundwater management option that meets the development ambitions and at the same time keeps the safe economic lifting depth as well. (C) 2015 Elsevier Ltd. All rights reserved.