Marine microdebris, in particular microplastics (plastics <5 mm), has become an issue of international concern due to its prevalence, persistence and potential adverse impacts on marine ecosystems. Informing source reduction based on ecological effects requires an understanding of the origin, distribution and characteristics of microdebris and the interactions with marine organisms. Here we show widespread contamination of the central Great Barrier Reef environment with microdebris, with microfibres comprising 86% of all items detected. Microdebris intake by coral reef fish was non-random, with chemical composition, shape and colour differing significantly from that detected in surface waters. Furthermore, the origin of microdebris contamination in surface waters is non-random with riverine discharge a likely source for microdebris detected at inshore, but not at offshore reef locations. Our findings demonstrate the complexities associated with determining marine microdebris exposure and fate, and assist in improving future ecological assessments and prioritizing source reduction.