In many studies, the research agronomists have been the designers of target systems, notably by using simulation models or prototyping methods. However, this role is being called into question as the farmers are more and more recognized as the actual designers of their agricultural systems. How, then, can agronomy support the farmer’s design capabilities and progressive transition towards innovative systems? What inputs (knowledge, methods, tools) should we, agronomists, bring or build to do that? To answer these questions, we analyse a case study, supported by research agronomists over several years, in which a collective of farmers had to redesign their agricultural systems to restore the quality of water in a catchment area (Prost et al., 2018).