Shellfish reefs support biodiversity, fisheries, and coastal protection; however, they are globally degraded. Understanding the drivers of assemblage structure and ecological functions is essential for effective conservation and restoration efforts. We investigated the spatial and habitat characteristics influencing fish communities, functional diversity, and key ecological functions, including shellfish recruitment, herbivory, and carnivory, at 10 intertidal shellfish reefs in Moreton Bay, central eastern Australia. Fish assemblages were shaped by habitat and spatial factors, particularly live oyster abundance, size variation, and proximity to seagrass. Functional diversity, richness, and ecosystem functioning peaked at sites with higher live oyster abundance (400 individuals/m²), lower mud cover (<25%), and minimal nearby intertidal area (<5 hectares within 500 m). Habitat features like reef vertical relief and patch size, along with spatial isolation from connected habitats, influenced ecological functions. Herbivory rates were higher at sites with greater vertical relief (from 0.7 to 1.7 g/72 hr), while oyster spat recruitment peaked in larger patches (60 to 180 recruits/m²). Carnivory was higher at less isolated reefs near subtidal channels (0 to 25 g/hr) and those with less muddy sediment (0 to 20 g/hr). These results emphasise the importance of habitat quality and spatial context in sustaining shellfish reef health.