Despite worldwide efforts to restore degraded mangrove forests in the past decades, defining and tracking restoration success remains a major challenge. In this study, we used a multi-isotope approach to trace ecosystem responses to forest clearing and replanting in a tropical mangrove forest reserve at Matang, Malaysia. We measured δ2H or δD deuterium, δ13C and δ15N (HCN isotopes) in common macroinvertebrate consumers (barnacles, prawns, gastropods, and crabs) across a 70-year chronosequence of mangroves. Functional food web recovery was indicated by a decrease in δ13C and δ15N and increase in δD for gastropod and crab consumers in older forests. Timing of this shift in food web isotopic signals took place between 5 and 15 years post-clearing of mangroves. These changes in food web function paralleled changes in crab community composition, but also reflected changes in physicochemical conditions within the forest, such as increased tree cover and shading, which resulted in a shift of the food web base from microalgal-derived to mangrove-derived organic matter. Prawns and barnacles from tidal waters adjacent to the mangrove forests were estimated to derive 17 to 25% of their nutrition from mangroves, primarily from a microbial loop that was processing localised dissolved and particulate organic matter exported from mangrove marshes. The top-down mixing model approach using combined HCN isotope measurements clearly separated inputs from mangroves versus microalgae for the first time in estuarine food web studies, and tracked ecological mangrove ecosystem recovery. This combination of tracers is recommended for future studies of mangrove conservation and restoration.