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Water resource management in arid agricultural irrigation regions is a great challenge for managers and decision makers. In some of those regions, many ponds have been built to ensure an adequate water supply for irrigation. Therefore, reservoirs and ponds should be managed conjunctively to minimize shortages of water. In this study, a new integrated mathematical model of conjunctive, or integrated, operation of reservoirs and ponds to maximize the water supply has been proposed for a reservoir-pond irrigation system. This objective has been achieved via the use of two models: an optimal model, which is used to determine the optimal discharge of reservoirs, and a simulation model, which considers the regulatory role of ponds and reservoirs and simulates their water supply to the irrigation system. An adaptive genetic algorithm has been employed in this study to solve the nonlinear and multi-dimensional reservoirs optimization problem. This methodology has been applied to the Yarkant River Basin to demonstrate its applicability, and three scenarios are presented. The main objective of the simulation-optimization model in the Yarkant River Basin is to minimize shortages in meeting irrigation demands for nine sub-irrigation systems subject to the constraint of ecological water transfer to the Tarim River. The optimizing effect of the model was particularly prominent under the third scenario, i.e., the XBD, MMK, and ART Reservoirs and 16 ponds conjunctively operated to meet the water demand of the YKB. The frequency of success (FS) in meeting agricultural water demands reaches up to 75%, and the value for ecological demand is 50.98%. The results demonstrate the importance of the conjunctive combined use approach for management of water resources in irrigation system of arid regions.