The conjunctive use of surface and groundwater resources is one alternative for optimal use of available water resources in arid and semiarid regions. The optimization models proposed for conjunctive water allocation are often complicated, nonlinear, and computationally intensive, especially when different stakeholders are involved that have conflicting interests. In this article, a new conflict-resolution methodology developed for the conjunctive use of surface and groundwater resources using Nondominated Sorting Genetic Algorithm II (NSGA-II) and Young Conflict-Resolution Theory (YCRT) is presented. The proposed model is applied to the Tehran aquifer in the Tehran metropolitan area of Iran. Stakeholders in the study area have conflicting interests related to water supply with acceptable quality, pumping costs, groundwater quality, and groundwater table fluctuations. In the proposed methodology, MODFLOW and MT3D groundwater quantity and quality simulation models are linked with the NSGA-II optimization model to develop Pareto fronts among the objectives. The best solutions on the Pareto fronts are then selected using YCRT. The results of the proposed model show the significance of applying an integrated conflict-resolution approach to conjunctive use of surface and groundwater resources in the study area.