<p>Phytoplankton are primary producers in freshwater ecosystems, forming the base of trophic networks. Some groups, such as cyanobacteria, have toxic potential, and their proliferation may be intensified by climate change, particularly warming, with significant impacts on aquatic food webs. Here, we examined how long-term adaptation to elevated temperatures influences competition among three taxa representing different phytoplankton groups: cyanobacteria (<i>Microcystis aeruginosa</i>), chlorophytes (<i>Desmodesmus armatus</i>), and diatoms (<i>Mayamaea permitis</i>), first in laboratory conditions and then in lake mesocosms. Our aim was to determine whether long-term adaptation changes the outcome of competition for phytoplankton groups when tested against each other, first in laboratory, then in lake-mesocosms. Heat adaptation increased the growth rates of cyanobacteria and chlorophytes in laboratory settings, whereas diatoms thrived in mesocosms. These contrasting responses emphasize the importance of studying aquatic ecosystems under natural conditions when assessing climate change impacts. Mesocosm experiments also revealed that environmental complexity—including light, temperature, and community interactions—plays a crucial role in cyanobacterial development. Our findings suggest that while long-term warming may favor cyanobacteria, its effects must be evaluated in a multi-species context. This study provides the first assessment of competitive interactions between these three species in mesocosm conditions simulating long-term global warming effects.</p>