Participatory processes provide opportunities for water professionals such as scientists and policymakers and other stakeholders such as the local communities and farmers to meet, exchange information, deliberate, and share values. There is a diversity of rapidly evolving participatory methods, here defined, as tools for supporting the process of designing nature-based solutions (NbS) together with the stakeholders. However, this requires a systematic and informed selection to facilitate the adequate choice of tools, aligned to the requirements and context of the water professionals and the stakeholders for the design and deployment of NbS. Despite this, there is still little progress and knowledge accumulation on how to select the most context-appropriate tool(s). Consequently, in this research, we propose a stepwise framework for the use of participatory tools, which we categorize as: (i) tools used for defining the hydro-meteorological hazards (HMH) and its impact on stakeholders—knowledge tools (ii) tools used for co-designing NbS with stakeholders—co-creation tools and (iii) tools used for co-implementing the transition towards NbS—transition tools. We then apply and test this stepwise framework on the participatory processes used in eight brook catchments distributed in four countries: the Netherlands, Belgium, France, and the United Kingdom. The framework is designed in steps that would lead to respectively: selecting, classifying, mapping, and grading the participatory tools leading to an informed and systematic decision of a tool or suite of tools for the design and deployment of NbS with stakeholders. With the application of this framework, we see that among the water professionals: (1) knowledge tools are central in the problem definition stage, particularly with non-technical stakeholders; (2) most anticipated co-creation tools are e-Tools/Virtual tools and workshops; (3) transition tools favor visual tools as a way of enabling the transition towards management practices.