Climate change can promote harmful cyanobacteria blooms in eutrophic waters through increased droughts or flooding. In this paper, we explore how water-level fluctuations affect the occurrence of cyanobacterial blooms, and based on the observations from case studies, we discuss the options and pitfalls to use water-level fluctuations for lake and reservoir management. A drawdown in summer causes an increase in retention time and increased water column nutrient concentrations and temperature of shallow water layers, which may lead to severe cyanobacterial blooms. This effect can potentially be counteracted by the positive response of submerged macrophytes, which compete for nutrients with cyanobacteria, with a higher chance of cyanobacterial blooms under eutrophic conditions. The balance between dominance by submerged macrophytes or cyanobacteria is temperature sensitive with stronger positive effects of drawdown as inhibition of cyanobacterial blooms expected in colder climates. Complete drying out reduces the amount of cyanobacteria in the water column after refilling, with lower water nutrient concentrations, lower fish biomass, lower abundance of cyanobacteria, higher transparency, and higher cover of submerged plants compared to lakes and reservoirs that did not dry out. Water-level rise as response to flooding has contrasting effects on the abundance of cyanobacteria depending on water quality. We conclude that water-level fluctuation management has potential to mitigate cyanobacterial blooms. However, the success will depend strongly on ecosystem properties, including morphometry, sediment type, water retention time, quality of inlet water, presence of submerged vegetation or propagules, abundance of fish, and climate.