Flood risk assessment is customarily performed using a design flood. Observed past flows are used to derive a flood frequency curve which forms the basis for a construction of a design flood. The simulation of a distributed model with the 1-in-T year design flood as an input gives information on the possible inundation areas, which are used to derive flood risk maps. The procedure is usually performed in a deterministic fashion, and its extension to take into account the design flood-and flow routing model uncertainties is computer time consuming. In this study we propose a different approach to flood risk assessment which consists of the direct simulation of a distributed flow routing model for an observed series of annual maximum flows and the derivation of maps of probability of inundation of the desired return period directly from the obtained simulations of water levels at the model cross sections through an application of the Flood Level Frequency Analysis. The hydraulic model and water level quantile uncertainties are jointly taken into account in the flood risk uncertainty evaluation using the Generalized Likelihood Uncertainty Estimation (GLUE) approach. An additional advantage of the proposed approach lies in smaller uncertainty of inundation predictions for long return periods compared to the standard approach. The approach is illustrated using a design flood level and a steady-state solution of a hydraulic model to derive maps of inundation probabilities. Copyright © 2016 John Wiley & Sons, Ltd.