Global eutrophication and climate warming exacerbate production of cyanotoxins such as microcystins (MCs), presenting risks to human and animal health. Africa is a continent suffering from severe environmental crises, including MC intoxication, but with very limited understanding of the occurrence and extent of MCs. By analysing 90 publications from 1989 to 2019, we found that in various water bodies where MCs have been detected so far, the concentrations were 1.4–2803 times higher than the WHO provisional guideline for human lifetime exposure via drinking water (1 µg/L) in 12 of 15 African countries where data were available. MCs were relatively high in the Republic of South Africa (averaged 2803 μg/L) and Southern Africa as a whole (702 μg/L) when compared to other regions. Values were higher in reservoirs (958 μg/L) and lakes (159 μg/L) than in other water types, and much higher in temperate (1381 μg/L) than in arid (161 μg/L) and tropical (4 μg/L) zones. Highly significant positive relationships were found between MCs and planktonic chlorophyll a. Further assessment revealed high ecological risk for 14 of the 56 water bodies, with half used as human drinking water sources. Recognizing the extremely high MCs and exposure risk in Africa, we recommend routine monitoring and risk assessment of MCs be prioritized to ensure safe water use and sustainability in this region.