Given the substantial effects of agricultural practices on the environment, this paper introduces a novel stakeholder-based framework for assessing the ecosystem services (ESs) provided by agricultural areas. Ecosystem services include essential functions such as water supply, food production, carbon storage, soil erosion control, and habitat support. In addition to ESs, water footprint is also taken into account to evaluate the impacts of agricultural activities on water resources. Some of the mentioned ESs are assessed using the Soil and Water Assessment Tool (SWAT). Then, by extending and combining the Conflict Resolution Model with the Composition of Probabilistic Preferences (CRMCPP) method and the leader-follower game (LFG), while considering the hierarchical structure of decision-makers, the best scenario for enhancing the ESs is selected. The Zarrinehroud River Basin (ZRB) in Iran has been chosen as a case study to evaluate the performance of the proposed framework, as this basin is vital for supplying water to Lake Urmia, the largest hypersaline lake in the Middle East. In this paper, 16 Water and Environmental Resources Management (WERM) scenarios have been defined according to the Urmia Lake Restoration National Committee (ULRNC) projects. Then, the mentioned ESs have been evaluated under different WERM scenarios. Ultimately, by utilizing the CRMCPP-LFG method and taking into account the hierarchical structure of decision-makers, we can identify the optimal WERM scenario. The criteria for making this decision include various factors, such as ecosystem services and the costs involved in implementing the WERM scenarios. In the selected scenario, the average water inflow into Lake Urmia is projected to rise to 1329 million cubic meters per year, which is 6.3% more than the average inflow in the current condition. Key initiatives in this scenario include reducing cultivated areas, altering irrigation methods, changing crop patterns, and incorporating water-efficient plant species.