The Hartbeespoort (HBP) Dam is a reservoir used for agricultural, domestic supply of raw potable water and recreational activities in South Africa's North-West Province. Eutrophication and cyanobacterial blooms have long been a cause of water-quality problems in this reservoir. The most prevalent bloom-forming species is Microcystis aeruginosa, often producing the toxin microcystin, a hepatotoxin which can negatively impact aquatic animal and human health, and poses a problem for potable water supply. Algal samples were collected monthly from four pre-determined sites in the dam during the summer months (December 2010-March 2011). Intracellular microcystins (MCs) were extracted using SPE C(18)cartridges, followed by separation, identification and quantification using LC-ESI-MS techniques. Quantitative variation studies of MCs were conducted with respect to MC congener isolated, sampling site and month. Three main MC congeners (MC-RR, -LR and-YR) were isolated, identified and quantified. In addition, three minor MCs (MC-WR, MC-(H(4))YR and (D-Asp(3), Dha(7))MC-RR were also identified, but were not quantified. The MC dominance followed the order MC-RR>MC-LR>MC-YR across all sites and time. The maximum and minimum concentrations were 268 µg/g and 0.14 µg/g DW for MC-RR and MC-YR, respectively, of the total MCs quantified from this study. One-way ANOVA showed that there were no significant differences between average MC concentrations recorded across months (P = 0.62), there was, however, a marginally-significant difference in concentrations among MC congeners (P = 0.06). ANCOVA revealed a highly significant interaction between sites and MC congeners on MC concentration (P < 0.001).