In order to deal with complex water management problems, it is increasingly claimed that researchers should collaborate with authorities and other stakeholders. According to the literature, such collaboration can enhance cognitive learning about the issues at stake, but there is little empirical evidence for this. In this paper, we assess whether collaborative research leads to more cognitive learning, and which factors may influence this. We first develop a structured methodology for assessing cognitive learning and identifying potential factors. Next, we apply this methodology in a case study on groundwater management in Delft (The Netherlands) and one on long-term flood management in the Lower Rhine area (Germany and The Netherlands). Contrary to some of the literature, our findings indicate that only intensive collaboration enhances cognitive learning. Therefore, we recommend organizing collaborative research only when all intended participants are sufficiently motivated to collaborate and learn. For these cases, we recommend to organise 1) many meetings, 2) intensive discussion of perspectives, 3) active participation in the research, and 4) an equal input in and influence on the research process by all involved actors.