Nuisance, toxic cyanobacterial blooms are a persistent and globally expanding problem. Prevention of blooms requires that external and internal sources of nutrients are managed to levels where development of cyanobacterial blooms is restricted. Control of blooms, in which their presence is reduced to a level where they no longer pose a risk through additional measures such as biomanipulation or artificial mixing, demands that three elements come together: (1) understanding of the key ecological traits of the dominant cyanobacteria taxa, (2) system analysis of the lake, in particular its morphometry, water and nutrient balance, (3) adequate design and execution of the management methods of choice. All three elements are important for choosing effective management interventions and predicting their outcome. Mitigation of blooms reduces the risks and harmful effects of blooms if they cannot be prevented or sufficiently controlled, methods such as harvesting of surface scums or application of cyanocides may be used in those cases where water quality improvement is urgent. Ultimately, managing cyanobacterial blooms is most effective in the context of developing a Water Safety Plan. This is a risk assessment and management approach developed by the World Health Organization and provides a platform for bringing together the stakeholders who have a say about activities in the catchment causing eutrophication. Together, they can develop and implement control measures in the chain from catchment to drinking-water offtake which effectively mitigate eutrophication and thus protect humans and the lake ecosystem services they rely on from effects of toxic cyanobacteria.