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This article analyzes learning processes resulting from the collective construction of a transdisciplinary research project, and from the implementation of a participatory approach to agricultural non-point source pollutions (nitrates and pesticides). The study is based on a participatory research project carried out in the Brie plain of Seine-et-Marne (France). It is regarded as a border-crossing process across disciplinary boundaries which often arbitrarily oppose researchers and stakeholders, as well as dividing the different stakeholders concerned by a public issue. The analysis first examines learnings resulting from a preliminary stage of participation co-engineering that involve scientists and their socio-professional partners, then learnings resulting from the participatory process with the local actors. The results show that the researchers and actors learn to shift their gaze from a technical object to a political one, linked to a rising awareness of the level of conflictuality which the participatory approach might assume. They also acquire new knowledge from the participating disciplines and from the local actors, as well as participatory skills. These learning processes may change everyone’s perceptions about the issue addressed, the territory and the actors involved. However, the study also revealed the limitations and learning assymetries of the process.