Tropical cyclones expose river basins to heavy rainfall and flooding, and cause substantial soil erosion and sediment transport. There is heightened interest in the effects of typhoon floods on river basins in northeast Japan, as the migration of radiocaesium-bearing soils contaminated by the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident will affect future radiation levels. The five main catchments surrounding FDNPP are the Odaka, Ukedo, Maeda, Kuma and Tomioka basins, but little quantitative modelling has been undertaken to identify the sediment redistribution patterns and controlling processes across these basins. Here we address this issue and report catchment-scale modelling of the five basins using the GETFLOWS simulation code. The three-dimensional (3D) models of the basins incorporated details of the geology, soil type, land cover, and used data from meteorological records as inputs. The simulation results were checked against field monitoring data for water flow rates, suspended sediment concentrations and accumulated sediment erosion and deposition. The results show that the majority of annual sediment migration in the basins occurs over storm periods, thus making typhoons the main vectors for redistribution. The Ukedo and Tomioka basins are the most important basins in the region in terms of overall sediment transport, followed by the other three basins each with similar discharge amounts. Erosion is strongly correlated with the underlying geology and the surface topography in the study area. A low permeability Pliocene Dainenji formation in the coastal area causes high surface water flow rates and soil erosion. Conversely, erosion is lower in an area with high permeability granite basement rocks between the Hatagawa and Futaba faults in the centre of the study area. Land cover is also a factor controlling differences in erosion and transport rates between forested areas in the west of the study area and predominantly agricultural areas towards the east. The largest sediment depositions occur in the Ogaki and Takigawa Dams, at the confluence of the Takase and Ukedo Rivers, and at the Ukedo River mouth. Having clarified the sediment redistribution patterns and controlling processes, these results can assist the ongoing task of monitoring radioactive caesium redistribution within Fukushima Prefecture, and contribute to the design and implementation of measures to protect health and the environment. Copyright (c) 2016 John Wiley & Sons, Ltd.