Landscape characteristics can influence the structure and functioning of faunal assemblages, yet our understanding of seascape effects on juvenile fish remains limited. This study investigated the role of seascape configuration in structuring juvenile fish assemblages (abundance, stability, and taxonomic distinctness) across the tropical seascape of the Dampier Archipelago, Western Australia. A combination of multivariate randomForest and full subsets modelling approaches were used to explore the importance of seascape, habitat, environmental, and biotic variables in explaining variation in structure of fish communities and the distributions of common taxa. Over half of the observed species were only recorded in a single habitat and thus each habitat contributed uniquely to the replenishment of the overall fish diversity within the seascape. Hydrodynamic conditions and seascape configuration strongly influenced community structure in both coral and macroalgal habitats. However, the conditions that maximised total abundance differed from, or opposed, those that optimised taxonomic distinctness. Individual species exhibited diverse responses to biophysical variables, and responses differed between coral and macroalgal habitats. These findings underscore the challenge of simultaneously managing for multiple ecological and economic goals coastal seascapes and support the use of conservation networks that encompass multiple habitats and areas that best support specific goals.