Ecosystems are increasingly degraded, fragmented and lost because of human activities globally. These impacts cause changes in the distribution of biodiversity and key ecological functions, modifications to food webs, and reductions in ecosystem condition and seascape connectivity. Understanding whether, and how, the spatial context (i.e. extent, position) and condition (i.e. structure and condition of patches, including habitat forming species) of ecosystems coalesce to support their function as animal habitats is critical for effective and cost efficient coastal management. These potential combined, or interactive, effects of spatial context and habitat condition on fish assemblages are, however, rarely quantified. We sampled fish assemblages from six different ecosystems (mangrove, seagrass, saltmarsh, log snag, rocky outcrop and unvegetated sediment) across 13 estuaries in eastern Australia and quantified the relative importance of spatial context and habitat condition variables for fish assemblage composition. Spatial context variables were consistently more important than habitat condition in structuring fish abundance and diversity. Sites that were closer to smaller vegetated habitats (i.e. mangrove and seagrass) and key seascape features (i.e. estuary mouth and intertidal flats) typically supported diverse fish assemblages in high abundance. While the composition of fish assemblages was primarily linked to spatial context variables, habitat condition variables that index food availability were also important for fish in mangroves, seagrass and rocky outcrops. Our results show that fish abundance and diversity are intimately linked to seascape connectivity and heterogeneity, and have important implications for conservation planning and fisheries management decisions in coastal ecosystems. We highlight the importance of quantifying the influence of the combined effects of habitat condition and spatial context for biodiversity across multiple ecosystems, and expect the outcomes to lead to more efficient and effective management planning.