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In the most of arid and semi-arid countries, the quality and quantity of available water resources play a significantly limiting role in development. In these regions, the conjunctive management is a suitable alternative that can lead to the optimal operation of available water resources. In this study, a conjunctive use model is developed in order to maximize water supply demands in 30-year period historical records. Discharge from resources, consumption priority in sectors and zones, inter-basin water conveyance plans and water demands are considered as the optimization model’s constraints. The ultimate goal of the study is to present short-term, medium-term and long-term operating policy. The sequential genetic algorithm is used to speed up the convergence to near global solution. The operating rules of surface and groundwater resources are separately developed for agriculture as well as domestic demands in the annual and monthly manner, respectively in the three above-mentioned periods. Finally, these rules are verified based on previously unused historical records. The results showed that the proposed model can effectively improve water resources potential, sustainable groundwater resources and undesirable use in agriculture sector.