The widespread investigations on water resources management has become an essential issue because due to lack of sufficient research and inattention to planning and management of conjunctive use of surface and groundwater. The conjunctive management is a suitable alternative for imbalanced water resources distribution and related constraints in using of surface water. In this paper, a multi-objective model is developed to maximize the minimum reliability of system as well as minimize the costs due to water supply, aquifer reclamation and violation of the reservoir capacity in operation and allocation priority. The non-dominated sorting genetic algorithm (NSGA-II) is used to present the optimal trade-off between the objectives. The sequential genetic algorithms is also applied (SGA) in order to be compared with the NSGA-II model. The results show that the NSGA-II model can considerably reduce the computation burden of the conjunctive use models in comparison with the SGA optimization model. The obtained trade-off curve shows that a little increase in reliability leads to much more system costs. The weighted single objective SGA model results verify optimal trade-off obtained from NSGA-II model and show the optimality of allocated discharges.