Coastal seascapes are increasingly impacted by human activities globally. These impacts occur over multiple spatial scales by proliferating ecosystem boundaries which change the extent, connectedness and condition of coastal ecosystems, altering their value for species. Disentangling the scales over which these impacts occur, and how the spatial context of natural habitats mediate these effects, can help to direct and prioritise coastal management. We quantified the relative effects of catchment, estuary and habitat level impacts on the structure of fish assemblages throughout south east Queensland. At broad landscape scales (i.e. catchment), we show that catchments with lower urban land area, and higher extents of diverse estuarine habitats consistently support a higher abundance and diversity of fish. At narrow spatial scales (i.e. seascape context and habitat condition), seascape context was more relatively important than habitat condition in structuring fish abundance and diversity. Sites that were closer to smaller vegetated habitats (especially mangrove and seagrass) and key physical attributes of estuaries (especially the estuary mouth) typically had higher fish abundance and diversity. Our results show that highly connected and heterogeneous seascapes support more abundant and diverse fish assemblages. Management that enhances these characteristics will maximise fish and fisheries value across coastal seascapes.