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Alpine rivers have been channelized by significant river training works in the past two centuries and are now disconnected from their natural environment. In adition, their flow regime is often affected by hydropower plant operation. Also the risk of flood damages is increasing continuously due to urbanization requiring additional flood protection measures. Nevertheless, such trained rivers still have high potential for renewable energy production. Furthermore, there is often a need for biotope restoration and creation of leisure infrastructures. New hydraulic schemes on such rivers have a chance to obtain public acceptance only if they are designed as multipurpose projects, which can alone ensure high synergies between different goals. Multipurpose projects are complex systems and have to be assessed with an appropriate global approach. Based on a network thinking approach, this article presents a global qualitative system analysis specially adapted for a typical multipurpose run-of-river power plant for the six project themes involved: (1) hydraulic scheme and river flow regime, (2) energy, (3) economy, (4) leisure activities, (5) groundwater and (6) ecology. The qualitative network thinking method developed by Gomez and Probst for business strategies is, for the first time, applied and enhanced for the assessment of such a multipurpose hydraulic scheme. Each theme, i.e. purpose of the project, is analysed separately, followed by a comprehensive study of the six themes combined together. Based on a network representation of the global system, three groups of factors are distinguished describing the sizes, the operations and the goals of the project. The size factors characterize the main geometrical aspects of the hydraulic structures, which can define the best layout of the project. The operation factors allow the optimization of the management of the reservoir. Finally, the objective factors characterize the synergies obtained by the multipurpose project. The developed methodology is illustrated with a case study of a multipurpose hydroelectric run-of-river power plant.