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The rapid rise of cyanotoxins production poses a serious threat to global freshwater ecosystems and has become an important issue of global public health. In Africa, a continent facing serious environmental problems, including poisoning by cyanotoxins, knowledge of the presence and distribution of these toxins remains limited. The primary objective of our review is to assess the occurrence and distribution of cyanotoxins, particularly microcystins (MCs), in African freshwater ecosystems. We aim to analyze the limited but existing literature on this subject, focusing specifically on studies published between 2001 and 2023. Recognizing the scarcity of research on this topic in Africa, we strive to elucidate the emerging patterns of toxin variants and their correlation with environmental variables, such as water temperature and nutrient concentrations. Our investigation reveals MCs as the predominant cyanobacterial secondary metabolites detected across the majority of African freshwater environments where cyanotoxins have been documented. Furthermore, their concentrations have exceeded the World Health Organization's (WHO) provisional guideline for lifetime human exposure through drinking water, which is set at 1 µg L−1, as indicated by data in Table 1. Highly significant positive relationships were found between toxin-producing cyanobacteria and environmental factors, in particular water temperature and nutrient concentrations. Given the associated exposure risks in Africa, we recommend frequent monitoring of water quality, the development of guidelines based on international best practice, toxicity tests, and epidemiological investigations to understand the health risks and impacts of cyanotoxin exposure. These measures are essential to both protect the well-being of humans and to ensure the sustainability of African aquatic ecosystems. [ABSTRACT FROM AUTHOR]