Water plants are well adapted to the aquatic environment due to the high plasticity of the photosynthetic apparatus of floating and submerged leaves. A strong decrease or complete disappearance of Nymphaea alba L. populations and their simultaneous replacement by Nuphar lutea L. Smith populations were observed for the last decades in freshwater ecosystems previously described as typical habitats of both species. However, there is no information on which environmental factors and / or interspecies differences between Nu. lutea and Ny. alba induce succession in Nymphaeaceae populations and decline of Ny. alba in natural habitats. We conducted a two-year comparative study of photosynthetic apparatus in floating leaves (chlorophyll fluorescence, leaf anatomy, and chloroplast ultrastructure) of both plant species in water bodies significantly different in the degree of anthropogenic impact and abundance of Nymphaeaceae individuals. It was shown that shifting of parameters of water chemistry induced by increasing concentrations of nitrogen and inorganic phosphorus did not affect photosynthetic processes in both species and confirmed literature data on high tolerance of rooted floating-leaved macrophytes to eutrophication. Irrespective of the water eutrophication level, a more rapid decrease of effective quantum yield (ΦPSII) of Nu. lutea floating leaves at irradiances above 500 μmol m−2 s−1 was observed. Active non-photochemical quenching (NPQ) mechanisms and local extensions of granal thylakoids indicate well-developed photoprotective features of Nu. lutea. The higher value of ΦPSII and diameter of grana in palisade parenchyma and a well-developed spongy parenchyma providing intensive gas exchange indicate better adaptation of photosynthetic apparatus of Ny. alba to high irradiance. In addition, leaf costs and leaf dynamics of Nu. lutea and Ny. alba can impact the outcome of the competition between the two species. © 2022 Elsevier GmbH