Water quality in France is highly degraded, and must be improved according to the European Water Framework Directive. As agriculture has been recognized liable for diffuse water pollution, measures have to be taken in water catchment areas, often including a redesign of cropping systems to efficiently limit nitrate and pesticides transfer to water while keeping an economically powerful agriculture. Such a redesign at a territorial scale raises methodological issues: who should be involved on the design process and how, to allow a sustainable and long-term change of local practices? Which knowledge should be used, in order to take into account the characteristics of the local situations? As the change is thought to last several years, which process should we start to favor actors’ learning? From two methods developed and implemented in six case studies, we analyzed the main characteristics and specificities of a process of design at territorial scale in order to be efficient