The Alfeios River, the longest and highest flow-rate river in Peloponnisos, constitutes an important water resource and ecosystem in Greece. In the present study, human activities in the Alfeios River Basin are described, and their impacts on water quality and the ecosystem are analyzed; effects resulting from interventions on river geomorphology between Flokas Dam and the river delta are determined. These actions have caused significant adverse impacts on the infrastructure (the dam, railroad, and road bridges), the level of aquifer water table and area water uses, and the aquatic and riparian ecosystem. A general integrated management strategy is formulated and a master management plan is proposed for resolving management problems in river basins. The plan considers local conditions and national requirements and complies with the European Communities legislation; it would help prevent further basin deterioration, improve water quality, and protect water resources and ecosystems in the area in accordance to sustainable development. The Alfeios River Basin serves as a case study in the development of the plan.