Coastal seascapes are increasingly impacted by human activities which occur over multiple spatial scales. These multi-scaled impacts change the extent, connectedness and condition of coastal ecosystems, and alters their value for species. Disentangling the scales over which these impacts occur, and quantifying how the spatial context of natural habitats mediate these impacts on fish assemblages, can help prioritise and optimise restoration efforts. We quantified the relative effect of catchment, estuary and habitat level impacts on fish assemblages throughout southeast Queensland. At broad landscape scales (i.e. catchment), we show that catchments with higher heterogenous natural habitat extent and lower chlorophyll-a concentrations consistently support a higher abundance and diversity of fish. At more narrow spatial scales (i.e. estuary context and habitat condition), spatial variables were more important than habitat condition in structuring fish abundance and diversity. Sites that were closer to vegetated habitat patches (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 maintaining natural catchments that can filter contaminants, combined with heterogeneous seascapes, support more abundant and diverse fish assemblages. Management that enhances these characteristics will maximise fish and fisheries value across coastal landscapes.