Water resources management issues tend to affect a variety of uses and users. Therefore, they often exhibit complex and unstructured problems. The complex, unstructured nature of these problems originates from uncertain knowledge and from the existence of divergent perceptions among various actors. Consequently, dealing with these problems is not just a knowledge problem; it is a problem of ambiguity too. This paper focuses on a complex, unstructured water resources management issue, the sustainable development—for ecology, economy and society—of the Delta-region of the Netherlands. In several areas in this region the ecological quality decreased due to hydraulic constructions for storm water safety, the Delta Works. To improve the ecological quality, the Dutch government regards the re-establishment of estuarine dynamics in the area as the most important solution. However, re-establishment of estuarine dynamics will affect other uses and other users. Among the affected users are farmers in the surrounding areas, who use freshwater from a lake for agricultural purposes. This problem has been addressed in a participatory decision-making process, which is used as a case study in this paper. We investigate how the dynamics in actors’ perceptions and the knowledge base contribute to the development of agreed upon and valid knowledge about the problem–solution combination, using our conceptual framework for problem structuring. We found that different knowledge sources—expert and practical knowledge—should be integrated to create a context-specific knowledge base, which is scientifically valid and socially robust. Furthermore, we conclude that for the convergence of actors’ perceptions, it is essential that actors learn about the content of the process (cognitive learning) and about the network in which they are involved (strategic learning). Our findings form a plea for practitioners in water resources management to adopt a problem structuring approach in order to deal explicitly with uncertainty and ambiguity.