The cyanobacterial diversity, biomass and nutrients (nitrite, nitrate and phosphate) of the Weija, Kpong, Owabi and Barekese reservoirs in Accra and Kumasi Metropolitan Areas of Ghana, were monitored from January to June 2006. The results show that the reservoirs were dominated by nanocyanobacteria not recorded in earlier studies. The Weija reservoir was the most diversified in terms of cyanobacterial species, which was dominated by the nanocyanobacterium Aphanocapsa nubilum accompanied by Merismopedia tenuissima, Planktolyngbya minor and Pseudanabaena recta. The Kpong reservoir was dominated by Geitlerinema unigranulatum, whilst the Owabi and Barekese reservoirs, both situated in the closed-forest region of Ghana with high rainfall and human activity, were dominated by the nanocyanobacterium Cyanogranis ferruginea, new for Ghana and for the whole of tropical Africa. A high and significant correlation was obtained between cyanobacterial abundance and nitrite in the Weija reservoir (r = 0.99) as well as phosphate (r = 0.58), whilst a negative correlation was obtained between cyanobacterial abundance and nitrate. In the Owabi reservoir, positive correlations were obtained between cyanobacterial abundance and the three nutrients (r = 0.85, 0.93 and 0.84, respectively). In the Kpong and Barekese reservoirs, low correlations were obtained between cyanobacterial abundance and the three nutrients. In the Kpong reservoir a high positive correlation was obtained between monthly rainfall and cyanobacterial abundance (r = 0.83). Intracellular microcystins have been identified in all four reservoirs.