A study which probed the occurrence and quantitative variations hepatotoxic microcystin in a Sub Saharan drinking freshwater reservoir was carried out between November 2014 and March 2015. Results reveal the presence of MCYST-YR, MCYST-LR, MCYST-RR, MCYST-LA and MCYST-LF variants either in cells collected directly from bloom or toxic isolates cultured under laboratory conditions. Two minor microcystin congeners (MCYST-(H-4)YR) and (D-Asp(3), Dha(7)) MCYST-RR) were identified, but not quantified. Variants dominance were in the order MCYST-LR > MCYST-RR > MCYST-YR > MCYST-LA > MCYST-LF across sampling sites. Maximum and minimum concentrations of quantified MCYSTs congeners were (489.25, 50.95 A mu g toxin/g DW), (98.92, 9.11 A mu g toxin/g DW), (140.25, 12.07 A mu g toxin/g DW), (56.99, 6.20 A mu g toxin/g DW) and (50.46, 3.65 A mu g toxin/g DW) for MCYST-LR, MCYST-YR, MCYST-RR, MCYST-LA and MCYST-LF, respectively. Analysis of variance (ANOVA) revealed there was a high significant difference between mean microcystin concentrations across sampling sites (p < 0.05).