The French-Swiss project SYNAQUA (INTERREG France-Switzerland 2017-2019) focuses on the development and the validation of genomic tools for water quality biomonitoring based on diatoms and oligochaetes. As part of the work-package dedicated to stakeholders and public awareness and involvement, three foresight participative seminars were organized in Lyon and Paris in early 2019. These seminars aimed to design various feared and desired scenarios of genomic tools development in France (and to a lesser extent in Switzerland), then to build an ideal but realistic one, favouring a better biomonitoring. The outcome of the seminars included an action plan along six fields of action: the development, experimentation and normalisation of methods based on eDNA; the regulation and organisation of biomonitoring allowing a good implementation of these tools; the training and mobilisation of professionals; the awareness-building and involvement of policy and decisions makers; the awareness-building and involvement of civil society; the set-up of an implementation mechanism for the overall plan, insuring a steady and consistent progress. The “ideal scenario”, based on a good complementarity between genomic and traditional methods, requires a strong collaboration between all the concerned professionals, especially between researchers and operators, as well as political will and funds to support the process of development. To secure such an involvement, it is necessary to demonstrate how these methods will improve the preservation and restauration of aquatic environments and the overall quality of life and health of the population, with an optimized use of financial resources.