Anthropogenic disturbances within or near aquatic ecosystems often contribute to eutrophication events. Cyanobacteria are a key group responsible for environmental problems associated with eutrophication processes. Interest is growing in estimating the threat of cyanobacteria in tropical Africa, however, there is still a lack of understanding regarding temporal drivers of cyanobacteria dynamics in natural aquatic ecosystems given the paucity of relevant fundamental research in this area. To better understand cyanobacteria dynamics, potential drivers of cyanobacteria dynamics were investigated in a model tropical reservoir system, whereby phytoplankton communities and water quality parameters were sampled during the tropical hot–wet, cool–dry and hot–dry seasons. Fifteen cyanobacteria taxa were recorded over the study period. Microcystis spp. and Cylindrospermopsis spp., known cyanotoxins producers, were the most prevalent bloom-forming taxa found in the study, with overall Cyanobacteria relative abundances being greatest during the cool-dry season. This was likely driven by decreased river inflows and increased reservoir mixing during the cool-dry period. Combinations of macrophyte cover, dissolved oxygen levels, water transparency, reactive phosphorus, water depth and chemical oxygen demand were found to significantly affect cyanobacteria community structure. The study highlights that under climate change forecasts (for much of tropical arid Africa), potentially harmful and problematic algal species may proliferate. Management options, therefore, need to be explored to maintain water quality and potable availability to mitigate against indirect harmful effects of environmental changes on ecosystems and human communities that utilise their services.