In this paper, a methodology is presented for managing hydrological ecosystem services by taking into account the hierarchy of stakeholders involved in the decision-making process. With this in mind, a water allocation model is first used for allocating water resources to demands. Then, several ecosystem services (ESs)-based criteria are defined to evaluate hydrological ESs of water resources management policies. A set of water and environmental resources management strategies (alternatives) are defined for decision-makers, and several drought management strategies are determined to decrease the area of key crops and water demands of agricultural nodes. To model a multi-agent multi-criteria decision-making problem for managing hydrological ESs, three main steps are considered as follows: • Different ES-based criteria (i.e., economic profit, NPP,1 and ecological index) are defined, and their grade-based values are estimated. • Several strategies are defined for stakeholders at different levels. • A recursive evidential reasoning (ER) approach, which considers a hierarchical structure for decision-makers and a leader-follower game, is used to select the best strategy for each decision-maker.The applicability and efficiency of the methodology are illustrated by applying it to a real-world case study. The methodology is general and can be easily applied to other study areas.