Increasing population has dramatically increased the request for agricultural products. In addition, lands and water resources with suitable quality are limited. Therefore, optimal allocation of limited resources to different demands has become very important in recent years. In this study, a model is developed to optimize a water resources allocation scheme considering the conjunctive use of surface water and groundwater resources, as well as determining a suitable crop pattern. The economic objective function of the optimization model is to maximize the net benefit, considering the water pumping cost, crop cultivation cost and the benefit of total crop production during the study time horizon. The effect of a marginal water deficit in the reduction of crop yield and water table fluctuations are considered. A genetic algorithm is used to solve the optimization model. The proposed model is applied to the Varamin plain to determine the optimal crop mix and water allocation from surface and groundwater. In order to evaluate the results of the model, the performance indices are calculated. The effect of imposed policies on the crop pattern is investigated through the definition of two scenarios and the results are compared. Also, the potential of the study area, for applying deficit irrigation strategies using economic analysis, is investigated.