In the face of complex and uncertain issues, one important goal of public participation in resource management and research is to foster communication and the inclusion of non-expert knowledge—thus the effective flow of information between project organisers and stakeholders. We compare different methods (instruments, tools) that were employed in the German–Austrian ‘PartizipA’ project to structure information flows in participatory processes. Depending on their goals and context, more or less ‘formalised’ and ‘participatory’ methods were applied, the most important being guided interviews, focus groups, agent-based modelling, nutrient modelling, cognitive mapping and group model building as well as the development of a common document. Two regional case studies, both concerned with European-induced institutional change, are portrayed in which the specific participatory methods were embedded. The Austrian case study involved the analysis and modelling of agricultural land use in the region of St. Pölten against the background of the reform of the Common Agricultural Policy, while the implementation of recent European water policy was the issue in the German agricultural region north of Osnabrück. Presenting both cases in their regional context, the applied methods are first described according to the logic of the entire respective process. Subsequently, the specific methods are systematically analysed and compared according to their objective, context and degrees of participation and formalisation. Finally, we evaluate all methods regarding their effectiveness in terms of goal attainment and their potential generalisation, seeking to respond to the question of when a particular method might best be used.