The European Water Framework Directive (WFD) constitutes a complex regulation that calls for numerous decisions under uncertainty on the part of the implementing agencies in the member states. This contribution first discusses two different types of uncertainty that may arise in the implementation of the WFD and identifies ways to manage them. Results of a text analysis show that uncertainties are not systematically addressed either in the directive itself or in CIS guidance documents. This paper shows that an important instrument to both manage and, where possible, reduce uncertainty is the participation of interested parties and the broader public. The focus lies on the perspective of the competent authority that has the responsibility to develop and implement the management plan. The paper concludes with recommendations of how to profit from public participation in managing uncertainty but also of where to look out for possible stumbling blocks.