Elevated CO₂ generally stimulates C₃-type photosynthesis, but it is unclear how an increase in CO₂ assimilation will interact with other factors that influence plant growth. In wetlands, the response of plants to elevated CO₂ will interact with soil saturation, particularly in forested wetlands where soil saturation is a strong regulator of plant productivity. We performed a four-month experiment to determine whether elevated CO₂ and flooding interact to influence the growth of a flood-tolerant tree (Taxodium distichum) and a flood-tolerant herbaceous emergent macrophyte (Orontium aquaticum). Seedlings were grown in glasshouses at two CO₂ levels (350 and 700 μL L⁻¹) crossed with two water depths (5 cm above and ≥5 cm below the soil surface). We hypothesized that elevated CO₂ would increase photosynthesis regardless of water depth and species; however, we also expected flooding to prevent elevated CO₂ from increasing the growth of the tree species due to O₂ limitation or other physiological stresses associated with reduced soil environments. We found that elevated CO₂ increased whole-plant photosynthesis in both species regardless of the flooding treatment. For T. distichum, this higher photosynthetic rate resulted in greater biomass only in the non-flooded treatment. This result suggests that some factor related to flooding constrained the biomass response of the flooded woody plants to elevated CO₂. In contrast, elevated CO₂ increased O. aquaticum biomass regardless of the flooding regime, perhaps because it occurs in wetter landscape positions than T. distichum and is less sensitive to flooding. We conclude that flooding may limit plant growth responses to elevated CO₂, particularly in woody plant species.