During the last century the mean sea level has been increasing at a rate of 0.2–0.4 mm·year⁻¹, and that rate is expected to accelerate during this century. Coastal wetland ecosystems are sensitive to the potential changes and impacts resulting from a rise in sea level. In the coastal region of the Gulf of Mexico, freshwater swamps are wetlands located further inland than mangroves, and while influenced by the tides, maintain freshwater conditions. Due to their location, the rise in sea level could increase the levels of flooding and salinity in these ecosystems. The objective of this study was to evaluate, under greenhouse conditions, the effect of nine flood and salinity treatments on the survival, growth, and increase in the biomass of Annona glabra (pond apple) seedlings (average height: 18.6 ± 1.61 cm). The treatments combined two factors: water level (Saturation, Flood, Flood-Drought) and salinity (0, 5 and 15‰). Seedling survival was greater under freshwater conditions. Increases in height and diameter, and leaf and biomass gain, were more significant under saturation and freshwater conditions. Based on our results, we conclude increased flood levels and salinity will negatively affect the natural establishment of A. glabra seedlings in freshwater swamps under a scenario of rising sea level.