The study investigates the impact of hydrological uncertainties and the related sensitivity of the hydrodynamic modelling results on flood hazard mapping. Uncertainties in flood frequency analysis (FFA), including anticipated impact of climate change and sensitivity to channel and floodplain roughness, were examined. The study area is the lower Vipava river, a transboundary catchment shared between Slovenia and Italy with variable floodplain topography. Sensitivity analysis revealed that uncertainty in FFA and river channel roughness significantly influenced the inundation spatial extent and inundation depth, the impact of floodplain roughness appears to be limited. The analysis shows that natural successional changes in river channel roughness substantially impact the results of a 10-year RP event, increasing flood extent by 45%. The increase in inundated areas is less pronounced for 100- and 500-year RP floods, with increases of 15% and 11%, respectively. The assessed probability of inundation based on scenario ensembles provided an informative identification of areas most susceptible to potential changes in flood hazard. Our findings highlight the need to address critical scenario ensembles that incorporate FFA uncertainty and hydraulic roughness sensitivity, leading to more informative flood hazard mapping for steering future land use planning.