Up to 80% of the plastics in the oceans are believed to have been transferred from river networks. Microplastic contamination of river sediments has been found to be pervasive at the global scale and responsive to periods of flooding. However, the physical controls governing the storage, remobilization and pathways of transfer in fluvial sediments are unknown. This means it is not currently possible to determine the risks posed by microplastics retained within the world's river systems. This problem will be further exacerbated in the future given projected changes to global flood risk and an increased likelihood of fluvial flooding. Using controlled flume experiments we show that the evolution of the sediment bed surface and the flood wave characteristics controls the transition from rivers being 'sinks' to 'sources' of microplastics under flood conditions. By linking bed surface evolution with microplastic transport characteristics we show that similarities exist between granular transport phenomena and the behavior, and hence predictability, of microplastic entrainment during floods. Our findings are significant as they suggest that microplastic release from sediment beds can be managed by altering the timing and magnitude of releases in flow managed systems. As such it may be possible to remediate or remove legacy microplastics in future.