Participatory modeling (PM) has become an essential concept in environmental impact assessment and planning in the field of water resources. In this paper, we focus on the use of PM to support the development of the integrated regional modeling system DANUBIA as a scientific concept to analyze the previously unknown impacts of global change, i.e., the combined effects of climate, demographic, economic, social and ecological change, on the Upper Danube Catchment (Germany). We use this case study to examine the specific conditions for PM in the field of complex integrated models on a regional scale. We describe the stepwise PM process and discuss the respective results, focusing on (1) the stakeholder dialogue's contribution in supporting the development of new, complex modeling systems, particularly on a regional scale, (2) conditions of stakeholder involvement in issues related to the distant future, such as climate change impacts on regional water availability, and (3) limitations of PM and scientists' motivation to carry out participatory research at all. We conclude that the PM process was not entirely successful in improving the scientific quality and practical applicability of the developed models because the process goals were manifold and overambitious, and the definition of the problem of ''global change impacts on a regional scale'' was too weak and uncertain to allow for a clear common objective of modelers and stakeholders. We claim that there is a lack of incentives for scientists, particularly natural scientists, to commit to PM activities.