We investigated the effects of elevated CO2 concentrations and longer tidal flooding duration on two-year-old Avicennia marina and Rhizophora stylosa seedlings for a full year. The seedlings were grown in greenhouses for ambient CO2 (400 ppm) and in enclosed CO2-controlled chambers, which were installed inside the greenhouses for elevated CO2 (800 ppm). The tidal flooding duration was set-up according to the species distribution in the intertidal zone in New Caledonia for the controlled treatment and was increased by 1 h 45 min for the experimental treatment. A total of 400 A. marina and 720 R. stylosa were monitored during this experiment. We measured heights and basal diameters of all seedlings every 90 days, and we determined the above and below ground biomass at the end of the experiment. Our results showed that elevated CO2 increased the growth rates of both A. marina and R. stylosa, for which the final biomass was, respectively, 46 and 32% higher than in the ambient CO2 treatment. We suggest that this increase was driven by a stimulation of photosynthesis under elevated CO2, as demonstrated in a previous study. Considering the tidal flooding duration treatment, we observed a contrasted effect between the species. Longer tidal flooding increased the growth of A. marina, whereas it reduced the growth of R. stylosa in comparison to the controlled treatment. This result may be related to the specific ecosystem zonation in this semi-arid climate, which limits water inputs into the Avicennia zone that increases the salt concentration in the soil, whereas Rhizophora is regularly submerged by tides due to its lower position in the intertidal zone. As a result, the combination of both treatments had a positive cumulative effect on the growth of A. marina. Although it was not the case for R. stylosa, the negative effect of longer tidal flooding on this species did not suppress the enhancement of growth resulting from elevated CO2 concentrations. At the end of the experiment, elevated CO2 increased the C:N ratios of the seedlings, thereby producing a more refractory organic matter, which will potentially result in lower decomposition rates and thus may increase carbon accumulation in mangrove soils. These results suggest that future climate changes may enhance the productivity of mangrove seedlings by increasing their growth, which may in turn increase the carbon storage potential of mangroves in their biomass.