Variability in supply of terrestrial sediments to the coastal zone impacts sediment transport processes and ecological dependencies. This study investigated surface sediment distribution and transportation within a 2020 km2 shallow embayment following a period of flood induced sediment supply. Extensive field sampling of 221 common sites between 2015 and the 2019 follow-up survey presented, identified significant reduction in fine sediment fractions, evident through a 367 km2 decrease in surface mud coverage. Wind-wave sediment transport processes controlled the spatial distribution of fine sediments, exporting 23 million tonnes of mud from the shallow sedimentation zones. In a broader context, sensitive benthic habitats such as seagrass meadows exhibited signs habitat recolonisation coinciding with areas of reduced mud content. Despite these promising short-term outlooks, the developed fine sediment budget suggests ongoing terrestrial sedimentation will exhaust key sediment sinks within Moreton Bay, effectively reducing the system’s ability to buffer future sedimentation events.