Integrated Management of the Water Resources is nowadays a prerequisite for environmental preservation and economic growth. The EU Water Framework Directive provides the guidelines to develop strategies and institutions to protect and restore the water resources in both qualitative and quantitative bases. However, the implementation of the proposed measures incorporates significant difficulties arising from the lack of necessary data, the fragmented approach often followed in water management and the incomprehension of the interactions between hydrologic systems and ecological components. In this particular study, a combination of remote sensing data, hydrologic models, ecological assessment techniques, GIS software and isotopic surveys have been adopted to extensively study the water resources of Trichonis Lake catchment, in Western Greece, in order to develop management alternatives aiming at protecting ecologically significant wetlands and meeting the local irrigation demands. The management alternatives have been developed with the contribution of local authorities by redistributing the monthly water outflows from the lake according to the ecological and anthropogenic demands and comprise five plans that attempt to minimize the environmental impacts from the regional water use while maintaining the economic activities unaffected.