1. We review and update recent observations of cyanobacteria-zooplankton interactions, identify theoretical and methodological limitations and evaluate approaches necessary for understanding the effects of increasing cyanobacterial blooms on plankton dynamics. 2. The emphasis on oversimplified studies using large-bodied Daphnia species, not previously exposed to cyanobacteria, has limited our understanding of how the plankton responds to proliferating blooms. This overlooks the great diversity in zooplankton traits, and the adaptability of planktonic grazers, that enables them to deal with toxic prey. 3. Under increasing temperature and nutrient loading, the zooplankton will be subjected to increasingly intense selection pressure to tolerate cyanobacteria. Short zooplankton generation times suggest that increased blooms may select for the rapid evolution of behavioural and physiological traits that improve tolerance. 4. As eutrophication intensifies, should we expect physiologically tolerant zooplankton that may be able to control blooms, or be concerned with the effects of selective grazers in stabilising blooms? 5. We conclude that the increasing frequency, duration and intensity of blooms will select for better adapted zooplankton that coexist with, rather than control, cyanobacteria. Future evaluations of cyanobacteria-zooplankton interactions should consider that increasing exposure to blooms induces phenotypic and genotypic traits improving zooplankton tolerance. Equally important will be studies of the ecophysiology of zooplankton species that coexist with prolonged blooms, rather than those of a few large-bodied generalist cladocerans. 6. Since cyanobacteria produce more than one toxic or inhibitory metabolite, the unsystematic designation of toxicity based on single well-identified compounds (e.g. microcystin) should be revised. 7. Overall, the coevolutionary interaction between cyanobacterial defences and zooplankton grazer responses emerges as a critical but understudied regulator of bloom dynamics.