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With water resource allocation criteria, the three main components are economic, ecological and sociological aspects, which are often conflicting with each other. Water resource allocation problem is analyzed via the development of a multi-criteria decision support system. The main techniques used are (1) multi criteria decision making (MCDM), (2) geographic information system (GIS) (3) multiregional computable general equilibrium (CGE) (4) Expert System (ES). The Decision Support System (DSS) proposed in this paper is an effective combination of GIS, CGE, ES, where the three modules have the joint interface and are connected by middlewares. The above three modules are united as a whole Multi-criteria Decision Support System of Water Resource (WRMCDSS).