Building with Nature (BwN) is an innovative approach in flood policy, which aims to use natural system dynamics and materials for the design and realization of flood management projects. However, as natural dynamics are inherently unpredictable, the use of BwN design principles requires a fundamentally different approach to uncertainty in flood management. In this paper, we identify and classify the key uncertainties in the development process of a specific project using BwN design principles: the Sand Engine. Our results indicate that uncertainty about the social implications of applying BwN design principles is more relevant for project development than uncertainty in the factual knowledge base of the natural system. Although uncertainty did not hamper project development in this specific case, the changes in project design evoked by the use of BwN principles do not seem to be followed by proper changes in the development process preceding the project's implementation: in the Sand Engine project's development process, uncertainty is evaluated rather similar as in the current flood management practices. We claim that new approaches towards dealing with uncertainty are needed, to successfully address the uncertainties typical to projects using BwN design principles.