Estuaries support numerous ecosystem services that are valued by people, including the provision of nursery and adult habitat for fisheries species. How variation in habitat connectivity, condition and extent modify the distribution and size of fisheries species across estuarine seascapes, and whether different size classes of fish prefer different estuarine habitats, often remains unknown. We used stereo remote underwater video systems in six coastal habitat types across five estuaries in southeast Queensland to measure the fork length of four fisheries species; yellowfin bream, mangrove jack, sand whiting and sea mullet. Three of the four species differed significantly in size between habitats. Sand whiting were largest on bare sediment and log snags, the sea mullet were largest in seagrass habitats and bream were largest on unvegetated sediments. Bream showed clear change in habitat preference as they grew, moving from structured mangrove forests and log snags to more open habitats. Conversely, mangrove jack did not differ in size between habitats, likely because they use estuaries broadly as nursery habitat. We show the importance of estuarine seascape heterogeneity to support species of fisheries values, and identify that variation across the seascape should be a focus when prioritising management aimed at enhancing fisheries value.