Structural diversity formed by dense, floating Stratiotes aloides stands, generates hotspots of biodiversity of flora and fauna in wetlands. However, only part of the populations become emergent and provide this important facilitation. Since it has been hypothesised that its buoyancy depends on the rates of underwater photosynthesis, we investigated the role of dissolved CO2 availability and PAR on photosynthesis, biomass production and buoyancy in a controlled greenhouse experiment. Photosynthesis and growth were strongly influenced by both PAR and CO2 availability. At low PAR, plants formed less biomass and produced no emergent leaves, even when CO2 was abundant. At low CO2 levels, S. aloides switched to HCO3- use, resulting in a lower photosynthetic O2 production, decreased emergent leaf formation and increased CaCO3 precipitation on its leaves, all of which impaired buoyancy. At high PAR, low CO2 availability resulted in slower colonisation of the water layer, whereas CO2 availability did not influence PAR-limited plants. Our study shows that site conditions, rather than the sole abundance of potentially facilitating species, may strongly determine whether or not they form the structure necessary to act as a facilitator for biodiversity in aquatic environments.