Global degradation of coastal ecosystems is influencing the provision of ecosystem services, including fisheries maintenance services. Degradation of the Australian coastal zone and its resources following European occupation has been recognised for some time. This includes the loss of ecologically important coastal wetlands, which have strong trophic and habitat links to fisheries. In NSW, structural flood mitigation works are a principle driver of the decline of coastal wetlands; however, little action has been taken to quantify the extent of decline due to limited information of the pre-European settlement extent of coastal wetlands. We use spatial data sets in GIS to quantify prime fish habitat and calculate the loss of fish habitat for the large coastal floodplains of northern NSW, which are significant contributors to the commercial and recreational fisheries of NSW. The technique is validated by comparison with early maps of wetland distribution. We identified pre-European distribution of available fish habitat of approximately 477,000 ha, of which 87,000 ha was identified as prime fish habitat. Approximately 62,000 ha of prime fish habitat was impacted by drainage of the coastal floodplains in association with flood mitigation works which intensified in the mid-1950s and were largely completed by 1971, equating to a loss of approximately 72 % of prime fish habitat. The declining value of the ecosystem services provided by prime fish habitat following drainage is likely to be substantial. Some actions have taken place to restore the functions of this habitat although significant opportunities remain to reverse this decline through management actions that restore natural drainage and reinstate tidal exchange. These actions become even more important as pressures on coastal wetlands increase with climate change and associated sea-level rise.