Many species move among distinct habitats to feed, shelter, reproduce, or disperse, connecting ecosystems and populations across land and seascapes. In coastal seascapes, juvenile fish movements link multiple habitats, forming interconnected nurseries. While the concepts of nursery habitats and ontogenetic habitat shifts are widely accepted, it remains unclear how seascape features influence habitat selection during ontogenetic shifts. To examine how seascape attributes influence nursery function, we surveyed fish from six nursery habitats (coastal mangroves, island mangroves, seagrass, back-reefs, fringing reefs, and isolated reefs) using stereo-remote underwater video stations. Surveys were conducted four times over two years along 200 km of the inshore Great Barrier Reef, Australia. Key fisheries target species exhibited distinct patterns of nursery seascape use, migrating from mangrove and/or back-reef environments to coral reefs with increasing body size. Variation in the composition and configuration of nursery habitats strongly influenced their abundance at different sizes. These seascape effects were evident across all habitats and were more important for nursery function than habitat cover or fishing protection. Our findings demonstrate that the composition and configuration of coastal seascapes strongly influence nursery function, highlighting the need for marine spatial planning to incorporate seascape-scale attributes for the effective management of coastal nurseries.