Abstract Context The distribution of animals is influenced by a complex interplay of landscape, environmental, habitat, and anthropogenic factors. While the effects of each of these forces on fish assemblages have been studied in isolation, the implications of their combined influence within a seascape remain equivocal. Objectives We assessed the importance of local habitat composition, seascape configuration, and environmental conditions for determining the abundance, diversity, and functional composition of fish assemblages across a tropical seascape. Methods We quantified fish abundance in coral, macroalgal, mangrove, and sand habitats throughout the Dampier Archipelago, Western Australia. A full-subsets modelling approach was used that incorporated data from benthic habitat maps, a hydrodynamic model, in situ measures of habitat composition, and remotely sensed environmental data to evaluate the relative influence of biophysical drivers on fish assemblages. Results Measures of habitat complexity were the strongest predictors of fish abundance, diversity, and assemblage composition in coral and macroalgal habitats, with seascape effects playing a secondary role for some functional groups. Proximity to potential nursery habitats appeared to have minimal influence on coral reef fish assemblages. Consequently, coral, macroalgal, and mangrove habitats contained distinct fish assemblages that contributed to the overall diversity of fish within the seascape. Conclusions Our findings underscore the importance of structural complexity for supporting diverse and abundant fish populations and suggest that the value of structural connectivity between habitats depends on local environmental context. Our results support management approaches that prioritise the preservation of habitat complexity, and that incorporate the full range of habitats comprising tropical seascapes.