Hydrodynamic river models are applied to design and evaluate measures for purposes such as safety against flooding. The modelling of river processes involves numerous uncertainties, resulting in uncertain model results. Knowledge of the type and magnitude of these uncertainties is crucial for a meaningful interpretation of the model results. Uncertainty in the hydraulic roughness due to bed forms is one of the main contributors to the uncertainty in the modelled water levels. The aim of this study was to quantify the uncertainty in the bed form roughness under design conditions and quantify the effect on the design water levels in the Dutch river Waal. Five roughness models that predict bed form roughness based on measured bed form and flow characteristics were extrapolated to design conditions. The results show that the 95% confidence interval of the predicted Nikuradse roughness values under design conditions ranges from 0.32 to 1.03 m. This uncertainty was propagated through the two-dimensional hydrodynamic model, WAQUA, by means of a Monte Carlo simulation for an idealized schematization of the Dutch river Waal. The uncertain bed form roughness results in an uncertainty in the design water levels, with a 95% confidence interval of 0.53 m, which is significant for Dutch river management practice. The uncertainty in the bed form roughness was mainly caused by a lack of knowledge about the physical process of bed form evolution that causes roughness. An improved estimation of bed form roughness can significantly reduce the uncertainty in the design water levels. Copyright © 2012 John Wiley & Sons, Ltd.