The European Union has the ambition to be the first carbonneutral continent by 2050. To fulfil this objective and integrate into the grid the large amount of power from solar and wind, Europe can rely upon the high storage and flexible capacity of hydropower. Thus, new reservoirs and innovative use of current reservoirs will be needed to provide an effective contribution to this unprecedented European Green Deal. The project Hydropower Europe, funded by the H2020 research programme, is tasked with identifying innovative uses of reservoirs and prioritizing the associated innovation actions targeting an energy system with high flexibility and renewable share. The project deliverables are a Research and Innovation Agenda (RIA) listing the top strategic research and innovation directions and a Strategic Industry Roadmap (SIR) addressing non-technical actions and requests for the hydropower sector. This paper describes the vision of the project: “Hydropower as a catalyst for the energy transition”. In Part I of this paper, the Green Deal and the role of hydropower were outlined and discussed. In this Part II, after highlighting the complex environment for hydropower in Europe, and the challenges of biodiversity, the main innovation and research directions extracted from the RIA and the main steps of the SIR for combining multipurpose hydropower, in a sustainable, efficient and cost-effective manner, are presented.