To date, most research on cyanobacterial blooms in freshwater lakes has focused on the pelagic life stage. However, examining the complete cyanobacterial life cycle—including benthic life stages—may be needed to accurately predict future bloom dynamics. The current expectation, derived from the pelagic life stage, is that blooms will continue to increase due to the warmer temperatures and stronger stratification associated with climate change. However, stratification and mixing have contrasting effects on different life stages: while pelagic cyanobacteria benefit from strong stratification and are adversely affected by mixing, benthic stages can benefit from increased mixing. The net effects of these potentially counteracting processes are not yet known, since most aquatic ecosystem models do not incorporate benthic stages and few empirical studies have tracked the complete life cycle over multiple years. Moreover, for many regions, climate models project both stronger stratification and increased storm-induced mixing in the coming decades; the net effects of those physical processes, even on the pelagic life stage, are not yet understood. We therefore recommend an integrated research agenda to study the dual effects of stratification and mixing on the complete cyanobacterial life cycle—both benthic and pelagic stages—using models, field observations and experiments.