Advected cyanobacteria, algal blooms and cyanotoxins have been increasingly detected in freshwater ecosystems. This review gives an insight into the present state of knowledge on the taxonomy, dynamics, toxic effects, human and ecological health implications of cyanobacteria, algal blooms and cyanotoxins in the East African Community lakes. The major toxigenic microalgae in East African lakes include Microcystis, Arthrospira, Dolichospermum, Planktolyngbya and Anabaenopsis species. Anatoxin-a, homoanatoxin-a, microcystins (MCs), cylindrospermopsin and nodularin have been quantified in water from below method detection limits to 81 µg L−1, with peak concentrations characteristically reported for the wet season. In whole fish, gut, liver and muscles, MCs have been found at concentrations of 2.4 to 1479.24 μg kg−1, which can pose human health risks to a daily consumer. While there have been no reported cases of cyanotoxin-related poisoning in humans, MCs and anatoxin-a (up to 0.0514 μg kg−1) have been identified as the proximal cause of indiscriminate fish kills and epornitic mortality of algivorous Phoeniconaias minor (lesser flamingos). With the unequivocal increase in climate change and variability, algal blooms and cyanotoxins will increase in frequency and severity, and this will necessitate swift action towards the mitigation of nutrient-rich pollutants loading into lakes in the region.