Climate change and eutrophication are two environmental threats that can alter the structure of freshwater ecosystems and their service functions, but we know little about how ecosystem structure and function will evolve in future scenarios of climate warming. Therefore, we created different experimental climate scenarios, including present-day conditions, a 3.0 °C increase in mean temperature, and a "heatwaves" scenario (i.e., an increase in temperature variability) to assess the effects of climate change on phytoplankton communities under simultaneous stress from eutrophication and herbicides. We show that the effects of climate warming, particularly heatwaves, are associated with elevated cyanobacterial abundances and toxin production, driven by a change from mainly nontoxic to toxic Microcystis spp. The reason for higher cyanobacterial toxin concentrations is likely an increase in abundances because under the dual pressures of climate warming and eutrophication individual Microcystis toxin-producing ability decreased. Eutrophication and higher temperatures significantly increased the biomass of Microcystis, leading to an increase in the cyanobacterial toxin concentrations. In contrast, warming alone did not produce higher cyanobacterial abundances or cyanobacterial toxin concentrations likely due to the depletion of the available nutrient pool. Similarly, the herbicide glyphosate alone did not affect abundances of any phytoplankton taxa. In the case of nutrient enrichment, cyanobacterial toxin concentrations were much higher than under warming alone due to a strong boost in biomass of potential cyanobacterial toxin producers. From a broader perspective our study shows that in a future warmer climate, nutrient loading has to be reduced if toxic cyanobacterial dominance is to be controlled.