In mountain areas, natural hazards, e.g., flooding, snow avalanches, droughts, and landslides are triggered by climate change, anthropization, and economic development. Nature-Based Solutions (NBSs) are attracting increasing interest as they are able to couple technical solutions against natural hazards with ecological and socio-economic resilience. On this matter, the four-year H2020 Innovation Action “PHUSICOS—According to Nature” (Grant Agreement nr. 776681) project aims to assess the effectiveness of NBSs and hybrid solutions to hinder hydro-meteorological events in rural and mountainous areas in Europe. Among the ongoing activities within the project, a multi-criteria tool was implemented to assess the effectiveness of NBSs measures from the technical, environmental, and socio-economic perspectives. In this work, the preliminary application of the assessment tool to the Isar River (DE) PHUSICOS concept case is discussed, with reference to an ex-post analysis of the flood risk management plan, comparing the performances of the implemented NBS project scenario against a potential grey solution.