In the present study, we investigated the changes to nekton communities with increasing mangrove forest age and relationships between nekton and the mangrove vegetation, mangrove sediments and environmental variables. The nekton community was assessed as a potential indicator for evaluating habitat functionality of mangrove planting programs. In all, 99 species from 52 families were captured, including crabs, shrimp, squid and fish. The crustacean assemblage was dominated by Portunidae and Penaeidae, whereas the fish assemblage was dominated by Atherinidae, Apogonidae, Hemirhamphidae, Tetraodontidae, Congridae, Sphyraenidae, Murraenidae, Ambassidae, Gerreidae, Clupeidae, Platycephalidae, Gobiidae, Mullidae and Plotosidae, with these families accounting for 90% of all individuals collected. The species composition, abundance and biomass of the nekton community were not significantly correlated with mangrove vegetation and sediment variables, but were significantly associated with environmental variables, particularly proximity to reef and tidal inundation. The lack of correlations suggests that the whole nekton assemblage was not a useful indicator in evaluating the progress of restoring habitat functionality in these planted mangroves. However, a significant interaction with mangrove vegetation was found for non-fish components of the nekton. As such, crustaceans, particularly of the Portunidae and Penaeidae families, were useful indicators for determining the habitat functionality of planted mangroves.