Estuaries are widely recognized as key habitats supporting nearshore secondary production and catch of commercial fisheries. In Queensland, some of these coastal marine habitats are protected by the declared fish habitat programme run by the Department of Primary Industries and Fisheries. Expected environmental changes for Australian estuarine systems include reduced freshwater flow, increased sedimentation and with them, a loss of connectivity. At present, the relationship between the protected declared fish habitat and habitat connectivity remains unknown. By comparing long term coastal fish catch data with geomorphic characteristics of coastal habitats structural connectivity was previously identified as a potential driver of commercial fish catch in Queensland. An ecology landscape approach was used for this study to identify potential fish habitat hotspots along the coastline of Queensland thus allowing better defined networks of declared fish habitats. A comparison between this approach and the current declared fish habitats demonstrated potential deficits and provided important insights for fisheries management. Declared fish habitats should be placed in coastal habitats with high structural connectivity to ensure sustainability of fisheries in light of environmental changes.