In this study, we examined interactive effects of elevated atmospheric CO2, concentrations, and increased tidal flooding on two mangroves species, Avicennia marina and Rhizophora stylosa. Leaf gas-exchange parameters (photosynthesis, transpiration rates, water-use efficiency, stomatal conductance, and dark respiration rates) were measured monthly on more than 1000 two-year-old seedlings grown in greenhouses for 1 year. In addition, stomatal density and light curve responses were determined at the end of the experiment. Under elevated CO2 concentrations (800 ppm), the net photosynthetic rates were enhanced by more than 37% for A. marina and 45% for R. stylosa. This effect was more pronounced during the warm season, suggesting that an increase in global temperatures would further enhance the photosynthetic response of the considered species. Transpiration rates decreased by more than 15 and 8% for A. marina and R. stylosa, respectively. Consequently, water-use efficiency increased by 76% and 98% for A. marina and R. stylosa, respectively, for both species, which will improve drought resistance. These responses to elevated CO2 were minimized (by 5%) with longer flooding duration. Consequently, future increases of atmospheric CO2 may have a strong and positive effect on juveniles of A. marina and R. stylosa during the next century, which may not be suppressed by the augmentation of tidal flooding duration induced by sea-level rise. It is possible that this effect will enhance seedling dynamic by increasing photosynthesis, and therefore will facilitate their settlements in new area, extending the role of mangrove ecosystems in carbon sequestration and climate change mitigation.