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To achieve social and economic sustainability in and and semi-arid areas under water scarce situations, it is vital to promote efficient use of water through improved management of water resources. This paper presents a swarm optimization based solution to a detailed operational model for short-term reservoir operation for irrigation of multiple crops. The model integrates the dynamics associated with the water released from a reservoir to the actual water utilized by crops at farm level. It takes into account the nonlinear relationship of root growth, soil heterogeneity, soil moisture dynamics for multiple crops, yield response to water deficit at various growth stages of the crops and economic benefits from the crops. As the developed model is a nonlinear one, it is solved using a novel global optimization technique, namely elitist-mutation particle swarm optimization (EMPSO). The model’s applicability is demonstrated through a case study of Malaprabha Reservoir system in Southern India. The performance of the model is examined for different water deficit conditions and the sensitivity of the crop yield is analysed for water shortage at various growth stages. Also, the consideration of economic benefits in the objective function and its effect on the water allocation decisions for multiple crops are studied. Consequently, the output from the model includes initial storages, releases, overflows and evaporation losses for each 10-day period on the reservoir side; and allocation of water, actual evapotranspiration and initial soil moisture for each crop for each 10-day period on the field side, thus facilitating decision making for optimal utilization of the available water resources.