Climate change scenarios predict that rivers, lakes, and reservoirs will experience increased temperatures, more intense and longer periods of thermal stratification, modified hydrology, and altered nutrient loading. These environmental drivers will have substantial effects on freshwater phytoplankton species composition and biomass, potentially favouring cyanobacteria over other phytoplankton. In this Review, we examine how several cyanobacterial eco-physiological traits, specifically, the ability to grow in warmer temperatures; buoyancy; high affinity for, and ability to store, phosphorus; nitrogen-fixation; akinete production; and efficient light harvesting, vary amongst cyanobacteria genera and may enable them to dominate in future climate scenarios. We predict that spatial variation in climate change will interact with physiological variation in cyanobacteria to create differences in the dominant cyanobacterial taxa among regions. Finally, we suggest that physiological traits specific to different cyanobacterial taxa may favour certain taxa over others in different regions, but overall, cyanobacteria as a group are likely to increase in most regions in the future. ► Climate change is predicted to favour cyanobacteria over other phytoplankton in freshwater ecosystems. ► We examined how cyanobacterial physiology may provide a competitive advantage. ► Different taxa, because of their traits, will respond to different aspects of changed climate. ► Cyanobacteria will most likely increase, but with noted taxa and geographical differences.