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The Ecosystem Management (EM) process belongs to the category of Multi‐Criteria Decision Making (MCDM) problems. It requires appropriate decision support systems (DSS) where “all interested people” would be involved in the decision making process. Environmental values critical to EM, such as the biological diversity, health, productivity and sustainability, have to be studied, and play an important role in modeling the ecosystem functions; human values and preferences also influence decision making. Public participation in decision and policy making is one of the elements that differentiate EM from the traditional methods of management. Here, a methodology is presented on how to quantify human preferences in EM decision making. The case study of the National Park of River Nestos Delta and Lakes Vistonida and Ismarida in Greece, presented as an application of this methodology, shows that the direct involvement of the public, the quantification of its preferences and the decision maker's attitude provide a strong tool to the EM decision making process. Public preferences have been given certain weights and three MCDM methods, namely, the Expected Utility Method, Compromise Programming and the Analytic Hierarchy Process, have been used to select alternative management solutions that lead to the best configuration of the ecosystem and are also socially acceptable.

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