Key coastal wetland habitats have been disconnected from the estuary across all developed estuaries in Australia due to a range of interventions. Natural services, such as fisheries production, are adversely affected with a resulting economic and community cost. We used a multi-disciplinary approach of correlating habitat area with fishery health/abundance and prioritising tidal habitat restoration to identify potential areas for rehabilitation and to quantify the likely benefits of repair. Saltmarshes had the highest value for fisheries production ($250,000 AUD.yr1) while the broader value of estuarine habitats was in excess of $3 million AUD.ya-1. The eco-hydrological assessment suggests that under present day conditions, 680 – 2155 hectares of intertidal habitats could be created by adjusting flow regimes via modifications to current drainage infrastructure. These modifications would have significant flow-on benefits to fishery productivity. Explicit cost-benefit analyses of rehabilitation projects for the areas identified could help managers and industry quantify the future benefit of these projects. Regardless of rehabilitation options, climate change and the associated sea level rise will have an impact on estuarine habitat cover and we suggest that a similar approach could be used to outline the value that would be lost from fisheries.