Climate change is likely to increase the frequency, intensity and duration of cyanobacterial blooms in many eutrophic lakes, reservoirs and estuaries. Bloom-forming cyanobacteria produce a variety of neurotoxins, hepatotoxins and dermatoxins, which can be fatal to birds and mammals (including waterfowl, cattle and dogs) and threaten the use of waters for recreation, drinking water production, agricultural irrigation and fisheries. Toxic cyanobacteria have caused major water quality problems, for example in Lake Taihu (China), Lake Erie (USA), Lake Okeechobee (USA), Lake Victoria (Africa) and the Baltic Sea.
Climate change favours cyanobacterial blooms both directly and indirectly. Many bloom-forming cyanobacteria can grow at relatively high temperatures. Increased thermal stratification of lakes and reservoirs enables buoyant cyanobacteria to float upwards and form dense surface blooms, which gives them better access to light and hence a selective advantage over nonbuoyant phytoplankton organisms. Protracted droughts during summer increase water residence times in reservoirs, rivers and estuaries, and these stagnant warm waters can provide ideal conditions for cyanobacterial bloom development.
The capacity of the harmful cyanobacterial genus Microcystis to adapt to elevated CO levels was demonstrated in both laboratory and field experiments. Microcystis spp. take up CO and  and accumulate inorganic carbon in carboxysomes, and strain competitiveness was found to depend on the concentration of inorganic carbon. As a result, climate change and increased CO levels are expected to affect the strain composition of cyanobacterial blooms.