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Groundwater is the unique source of fresh water in El-Farafra Oasis, western desert, Egypt. The increasing demand of groundwater in El-Farafra Oasis has resulted in an indiscriminate exploitation of this source causing environmental hazards such as decline of groundwater levels and well interference. In this paper, the study of these problems is conducted. The methodology introduced in this paper includes application of mathematical and Genetic Algorithm (GA) techniques. This situation has led to a growing realization that through good management, use of groundwater can be made more productive and sustainable. The proposed model of optimization is based on the combination of the MODFLOW with GA. The performance of the proposed model is tested on groundwater management problem (maximization of total pumping rate from an aquifer at steady-state). The results show that the GA solutions nearly agree with the solutions of other methods of previous works. Thus, it can be used to solve the management problems in groundwater. This model is used to develop the optimal pumping rate and number of wells in El-Farafra Oasis under different scenarios. The results show that under the current situation, the optimal pumping rate is 183023 m(3)/day. The second scenario assumes an increase of number of wells by 20%, the optimal rate reaches 220016 m(3)/day. The third scenario proposes pumping rate 254484 m(3)/day which equalizes an increase in the cultivated area by 4000 acres, the optimal rate reaches 258007 m(3)/day.