Global warming is likely to exacerbate future fluvial floods in the world’s mega-delta regions due to both changing climate and rising sea levels. However, the effects of sea level rise (SLR) on fluvial floods in such regions have not been taken into account in current global assessments of future flood risk, due to the difficulties in modeling channel bifurcation and the backwater effect. We used a state-of-the-art global river routing model to demonstrate how these complexities contribute to future flood hazard associated with changing climate and SLR in the world’s largest mega-delta region, the Ganges-Brahmaputra-Meghna Delta. The model demonstrated that flood water in the main channels flows into tributaries through bifurcation channels, which resulted in an increase in inundation depth in deltaic regions. We found that there were large areas that experienced an increase in inundation depth and period not directly from the SLR itself but from the backwater effect of SLR, and the effect propagated upstream to locations far from the river mouth. Projections under future climate scenarios as well as SLR indicated that exposure to fluvial floods will increase in the last part of the 21st century, and both SLR and channel bifurcation make meaningful contributions.