The phytoplankton community in three small (0.065–0.249 km2) reservoirs in the stepped plateau landscape in the Kinangop area above the Rift Valley floor in Kenya were studied between 1998 and 2000. Approximately 70 species of phytoplankton were identified. The community was dominated by chlorophytes, cyanobacteria and chrysophytes. Diatoms were rare. The phytoplankton assemblage was frequently dominated by cyanobacteria in the dry season. The phytoplankton assemblage transformed to a mixture of cyanobacteria, chlorophytes and chrysophytes at the onset of the long rains, and mixture of cyanobacteria and chlorophytes after the long rains. Thereafter the phytoplankton assemblage consisted mainly of a mix of cyanobacteria and chrysophytes until the onset of the short rains when cyanobacterial dominance re-emerged. The most common phytoplankton species included Microcystis spp., Botryococcus braunii, Ceratium hirundinella, Anabaena spp. and Euglena viridis. The dry season cyanobacterial blooms produced cyanotoxins that included microcystin and endotoxins. The concentrations were well above the recommended safe limits for drinking water. The patterns of cyanotoxin production showed that the growth of the toxin-producing cyanobacteria was regulated by water temperature, pH and nutrients. The appearance of cyanotoxins in the small reservoirs is a serious public health issue in rural Kenya because such reservoirs are key sources of water for humans, livestock and wildlife.