© 2017 Springer Science+Business Media B.V., part of Springer Nature A comprehensive flood risk assessment should aim not only at quantifying uncertainties but also the variability of risk over time. In this study, an efficient modelling framework was proposed to perform probabilistic hazard and risk analysis in dike-protected river systems accounting for morphological variability and uncertainty. The modelling framework combined the use of: (1) continuous synthetic discharge forcing, (2) a stochastic dike breach model dynamically coupled to a stochastic unsteady one-dimensional hydraulic model (MIKE1D) describing river flows, (3) a catalogue of pre-run probabilistic inundation maps (MIKE SHE) and (4) a damage and loss model (CAPRA). The methodology was applied using continuous simulations to a 45-km reach of the Upper Koshi River, Nepal, to investigate the changes in breach and flood hazards and subsequent risks after 2 and 5 years of probable river bed aggradation. The study results indicated an increase in annual average loss of 4% per year driven by changes in loss distribution in the most frequent loss return periods (20–500 years). The use of continuous simulations and dike breach model also provided a more robust estimation of risk metrics as compared to traditional binary treatment of flood defence and/or the direct association of flow with loss return periods. The results were helpful to illustrate the potential impacts of dynamic river morphology, dike failure and continuous simulation and their significance when devising flood risk study methodologies.