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Severe water scarcity in recent years has magnified the economic, social, and environmental significance of water stress globally, making optimal planning in water resources necessary for sustainable socio-economic development. One of the regions that is most affected by this is the Sistan region and its Hamoun wetland, located in south-east Iran. Water policies are essential to sustain current basin ecosystem services, maintaining a balance between conflicting demands from agriculture and the protection of wetland ecosystems. In the present study, a multi-objective optimization model is linked with the Water Evaluation and Planning (WEAP) software to optimize water allocation decisions over multiple years. We formulate and parameterize a multi-objective optimization problem where the net economic benefit from agriculture and the supply of environmental requirements were maximized, to analyze the trade-off between different stakeholders. This problem is modeled and solved for the study area with detailed agricultural, socio-economic, and environmental data for 30 years and quantification of ecosystem services. By plotting Pareto sets, we investigate the trade-offs between the two conflicting objectives and evaluate a possible compromise. The results are analyzed by comparing purely economic versus multi-objective scenarios on the Pareto front. Finally, the disadvantages and advantages of these scenarios are also qualitatively described to help the decision process for water resources managers.