Climate change is expected to increase the frequency and magnitude of river floods1. Floods not only cause damage by inundation and loss of life2,3 but also jeopardize infrastructure because of bank failure and riverbed erosion processes that are poorly understood. Common flood safety programs include dike reinforcement and river widening4–9. The 2021 flood in the Meuse Basin caused 43 fatalities and a multibillion-dollar damage to infrastructure10. Based on analysis of the Meuse flood, we show how uneven widening of the river and heterogeneity of sediment deposits under the river can cause massive erosion. A recent flood safety program widened the river11, but created bottlenecks where widening was either prevented by infrastructure, or not yet implemented. Riverbed erosion was exacerbated by tectonic uplift that had produced a thin top gravel layer above fine-grained sediment. Greatly enhanced flow velocities produced underwater dunes with troughs that broke through the gravel armour in the bottlenecks, exposing easily erodible sands, resulting in extreme scour holes, one over 15 m deep. Our investigation highlights the challenges of re-engineering rivers in the face of climate change, increased flood risks, competition for river widening space, and calls for a better understanding of the subsurface.