Risk zonation maps are mostly derived from design floods which propagate through the study area. The respective delineation of inundated flood plains is a fundamental input for the flood risk assessment of exposed objects. It is implicitly assumed that the river morphology will not vary, even though it is obvious that the river bed elevation can quickly and drastically change during flood events. The objectives of this study were to integrate the river bed dynamics into the flood risk assessment procedure and to quantify associated uncertainties. The proposed concept was applied to the River Ill in the Western Austrian Alps. In total, 138 flood and associated sediment transport scenarios were considered, simulated and illustrated for the main river stem. The calculated morphological changes of the river bed at the moment of peak flow provided a basis to estimate the variability of possible water surface levels and inundation lines which should be incorporated into flood hazard assessment. In the context of vulnerability assessment an advanced methodological approach to assess flood risk based on damage probability functions is described.