AbstractTwo‐dimensional hydrodynamic models are frequently used for flood protection studies to compute inundation patterns and to estimate potential economic damage. However, the modelling of river processes involves numerous uncertainties. Knowledge of the type and magnitude of uncertainties is crucial for a meaningful interpretation of the model outcomes and its usefulness in decision making. The objective of this study was to quantify the uncertainty in the design water levels due to uncertain bed form and vegetation roughness for the Dutch River Waal. We quantified and combined these sources of uncertainty by means of a Monte Carlo simulation. The results showed that the 95% confidence interval of the design water levels is 0.49 m, 0.34 m and 0.12 m for bed form, vegetation classification and vegetation roughness parameterisation, respectively, and approximately 0.68 m for the combined roughness. These uncertainties are significant in view of Dutch river management practice.