Water quality preservation programmes as currently proposed by public institutions are questionable with regards to efficient territorial development, yet necessary in catchment areas, and for the improvement of water quality. We provide a method based on a multi-criteria and multi-stakeholder analysis to assess cropping systems designed with farmers in a vulnerable drinking water catchment. Individual interviews with various stakeholders involved in the catchment improvement programme allowed us to gather a diversity of points of view on their preferences concerning various criteria describing cropping system sustainability and economic, social and environmental aspects. Five groups of stakeholders with different preferences were identified to define five scenarios of sustainability preferences. To support a result-oriented approach, achievable goals to improve water quality and contribute to sustainable development were chosen together with stakeholders. Then cropping systems designed with local farmers were assessed using the five scenarios of stakeholders’ preferences to open discussions on the implementation of alternative cropping systems within the drinking water catchment. The method was able to identify some cropping systems that, although very diverse, might assure the required drinking water quality, and were judged as theoretically highly sustainable by all the stakeholder groups.