Cyanobacteria are known for their extensive and highly visible blooms in rivers or dams in Africa. One of the most important cyanobacteria is Microcystis aeruginosa which can synthesise various microcystins that may affect the health of humans and animals. Accurate and efficient detection of microcystins in water is thus important for public and veterinary health. Two enzyme-linked immunosorbent assays (ELISA), a commercially-available ELISA kit (Abraxis) and a newly-developed Norwegian ELISA (putatively cheaper and more robust) were used to detect microcystins in fresh water in South Africa. Water samples were collected monthly at two sites, the Hartbeespoort Dam and a crocodile breeding dam. Extremely high microcystin concentrations (exceeding 360 μg L−1) were detected in the Hartbeespoort Dam during January 2015, whereas the microcystin concentrations in the crocodile breeding dam peaked during March–April 2015. Both ELISAs were positively correlated when analysing water samples ‘as is’ and following resin adsorption and methanol extraction. However, following resin adsorption and methanol extraction of the water samples, the correlation between the two assays was much stronger. These results suggests that the two ELISAs provide comparable results. If the Norwegian-developed ELISA can be packaged and made available as a user-friendly kit, it could be used successfully in surveillance programmes to monitor microcystin concentrations in fresh water bodies in Africa.