Increased abstraction from the aquifer, in addition to the progressive drawdown of groundwater table can increase the concentration of pollutants. This research, optimal scenario for withdrawing water from wells is proposed for the aquifer sustainable development. The aquifer quantitative and qualitative simulation was carried out with the GMS model. The developed code in MATLAB2018b provides the link between the simulation and the NSGA-II optimization tools. Optimal scenario was chosen based on applying the Multiple-Criteria Decision Making (MCDM) and Berda Aggregation Method (BAM). The results show that reducing the current withdrawal rate to 51.55% can establish the quantitative and qualitative stability of the aquifer. The spatial and temporal distribution of nitrate concentration after applying the optimal discharge of wells shows that the nitrate concentration in central and eastern parts of the aquifer have greatly reduced. The developed structure can be used to improve the quantitative and qualitative status of any aquifer.