Transdisciplinary research offers a promising approach to development cooperation programs by integrating knowledge from academic and non-academic stakeholders, and from natural and social sciences. In the context of development research on water, there is little evidence on how stakeholder involvement takes place in the three stages of transdisciplinary research (problem definition, knowledge production, and knowledge application). This paper aims to create empirical evidence and insights on this question based on the Palestinian-Dutch Academic Cooperation Programme on Water (PADUCO). Six research projects, which have been implemented within the first phase of PADUCO, were examined using the data collected through a survey and document reviews. The results show that research problems were defined according to societal needs and contextual factors. Research teams were multidisciplinary and included non-academic members, whereas the institutional involvement of non-academic stakeholders was limited and unbalanced between the governmental and non-governmental actors. Although the application of the knowledge produced was mainly focused on academia, opportunities for broad dissemination were utilized, albeit to a limited extent. Finally, there was a lack of monitoring and evaluation of impacts, which is explained by the budget and time limitations of such small-scale projects and can be mitigated by programme-level measures.