Estuaries are a key coastal ecosystem providing social, economic and environmental benefits to the community. However, estuaries have suffered historical degradation due to extensive human activities. There has been an increase in habitat restoration efforts with Commonwealth, State and local governments funding a variety of projects aimed at returning ecological function and resilience to estuarine systems. Here we review the application of multiple metrics to infer the recovery of estuaries, following on-ground works. Biodiversity assessments quantify species presence and abundance, stable isotope analysis provides analysis of foodwebs, including the contribution of vegetated habitats to species productivity, and imaging sonars can infer fish movement, including both abundance and biomass. These metrics can provide insight on the recovery, and rate of recovery, of both specific habitats and entire systems. In Burrill Lake, NSW, the contribution of saltmarsh to the diet of glassfish increased by ~10% following habitat restoration. At Baker Creek, SA, species specific isotopic signatures of fish and crustaceans varied between saltmarsh and muddy shorelines, which is expected to change following recent reconnection of a previously disconnected coastal wetland. These studies provide crucial information for managers to inform ecosystem restoration and evaluate ecosystem services such as provisioning of fish stocks.