Cyanobacteria have a long evolutionary history that has been instrumental in allowing them to adapt to long-term geochemical and climatic changes, as well as current human and climatic alterations of aquatic ecosystems; e.g. nutrient over-enrichment, hydrologic modifications and warming. Harmful (toxic, hypoxia-generating, food web altering) cyanobacterial bloom (CyanoHAB) genera are particularly adept at taking advantage of these changes and perturbations. In addition, they have developed numerous mutualistic and symbiotic associations with other microbes and higher flora and fauna, and they modulate positive biogeochemical feedbacks, instrumental in their survival and dominance in diverse ecosystems. CyanoHABs are controlled by the combined and often synergistic effects of nutrient (nitrogen and phosphorus) inputs, light, temperature, water residence/flushing times, and biotic interactions. Accordingly, mitigation strategies are oriented towards manipulating these dynamic factors. Physical, chemical (nutrient) and biological manipulations can be effective in reducing CyanoHABs. However, these manipulations should also be accompanied by nutrient (both nitrogen and phosphorus in most cases) input reductions to ensure long-term success and sustainability. A major research and management goal for long-term control of CyanoHABs is to develop strategies that are adaptive to climatic variability and change, because nutrient-CyanoHAB thresholds are likely to be altered in a climatically more extreme world