In freshwater systems, cyanobacteria are strong competitors under enhanced temperature and eutrophic conditions. Understanding their adaptive and evolutionary potential to multiple environmental states allows us to accurately predict their response to future conditions. To better understand if the combined impacts of temperature and nutrient limitation could suppress the cyanobacterial blooms, a single strain of Microcystis aeruginosa was inoculated into natural phytoplankton communities with different nutrient conditions: oligotrophic, eutrophic and eutrophic with the addition of bentophos. We found that the use of the bentophos treatment causes significant differences in prokaryotic and eukaryotic communities. This resulted in reduced biodiversity among the eukaryotes and a decline in cyanobacterial abundance suggesting phosphorus limitation had a strong impact on the community structure. The low temperature during the experiment lead to the disappearance of M. aeruginosa in all treatments and gave other phytoplankton groups a competitive advantage leading to the dominance of the eukaryotic families that have diverse morphologies and nutritional modes. These results show cyanobacteria have a reduced competitive advantage under certain temperature and nutrient limiting conditions and therefore, controlling phosphorus concentrations could be a possible mitigation strategy for managing harmful cyanobacterial blooms in a future warmer climate.