The continuous degradation of mangrove habitats has encouraged governments and multi-lateral agencies to undertake rehabilitation initiatives to foster the recovery and biodiversity of these areas. However, some rehabilitation initiatives suffer high mortality because of incorrect species-site matching and failure to recognize the ecophysiology of mangrove species. This study investigated the effects of salinity, water depth and inundation on the growth, biochemical stress responses, and ecophysiology of Rhizophora stylosa in greenhouse conditions. Propagules were cultured in aquarium tanks and irrigated with low (0 ppt), moderate (20 ppt), and high (35 ppt) salinity treatments. In the first setup, the seedlings were cultured in aquarium tanks and arranged on the top of a platform at different elevations, subjecting the seedlings to flooding with low-water (3-5 cm), mid-water (10-13 cm) and high-water (30-33 cm) levels for ten months. In another setup, the seedlings were cultured for 15 months at the low-water level and subjected to inundation hydroperiods: semi-diurnal, diurnal and permanent inundation for one week. These microcosms simulated emerged and submerged conditions, mimicking intertidal inundation that seedlings would experience. The results showed that salinity significantly affected the early development of the cultured seedlings with higher growth rates and biomass at low and moderate salinity than those at high salinity. Levels of reactive oxygen species (ROS) and antioxidant activities (AOX) were significantly lower in the emerged condition than those in an inundated condition. Inundation imposed a higher-degree of stress than that of the salinity effect, with prolonged inundation caused sublethal damage (chlorotic leaves). Furthermore, inundation caused the reduction of photosynthetic pigments and fluorescence, dependent on salinity. Extrapolating the ecophysiology of R. stylosa, this species had low tolerance to inundation stress (high ROS and AOX, reduced pigments). Translating this low tolerance to field conditions, in the frequently inundated areas (i.e., seafront mangrove fringes) that are subjected to longer inundation at spring tides, this species may suffer from oxidative stress, stunted growth and consequently low survival.