The Water Framework Directive (WFD) imposes a new approach to water resource management in the EU states. Uncertainty surrounding its implementation, however, could badly affect the achievement of the objectives set by the Directive. Although not directly linked to a set of techniques to deal with it, the WFD and accompanying guidance documents mention uncertainty as a relevant factor in implementing the WFD and especially in the context of economic analysis of water uses. In this paper we review several sources of uncertainty surrounding economic analysis focusing on uncertainty related to socioeconomic descriptors of river basins and water uses and uncertainty surrounding the selection of measures (WFD article 11). While a number of sources of uncertainty in socioeconomic descriptors of river basins and water uses are discussed, we argue that the transformation of this information into hydrological spatial units may turn out to be a real challenge for uncertainty assessment. For the choice of the most appropriate measures, we distinguish between uncertainty being 'internalised' in decisions (by using stochastic decision methods) and uncertainty stemming from the application of these methods.