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In the present study, an integrated soil water balance algorithm was coupled to a non-linear optimization model in order to carry out water allocation planning in complex deficit agricultural water resources systems based on an economic efficiency criterion. The LINGO 10.0, optimization package has been used to evolve at optimal allocation plan of surface and ground water for irrigation of multiple crops. The proposed model was applied for Qazvin Irrigation Command Area, a semi-arid region in Iran. Various scenarios of conjunctive use of surface and ground water along-with current and proposed cropping pattern have been explored. Some deficit irrigation practices were also investigated. The results indicate that conjunctive use practices are feasible and can be easily implemented in the study area, which would enhance the overall benefits from cropping activities. The study provides various possible operational scenarios of the branch canals of the command area in the common and dry condition, which can help managers in decision making for the optimum allocation plans of water resources within the different irrigation districts. The findings demonstrate that for deficit irrigation options, the mining allowance of ground water value of the command area is greatly reduced and ground water withdrawal may be also restricted to the recharge to maintain the river-aquifer equilibrium.