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In this paper, a methodology for conjunctive use of surface and groundwater resources is developed using the combination of the Genetic Algorithms (GAs) and the Artificial Neural Networks (ANNs). Water supply, reduction of pumping costs and controlling the groundwater table fluctuations are considered in the objective function of the model. In the proposed methodology, the results of the PM groundwater simulation model are used to train the ANNs based simulation model. This model is then linked to the GA based optimization model to develop the monthly conjunctive use operating policies. The proposed model is applied to the surface and groundwater allocation in the irrigation networks in the southern part of Tehran, the capital city of Iran. The results of the proposed model show the significance of an integrated and systems approach to surface and groundwater resources allocation in the study area.