Background: Microcystins are cyclic peptides containing seven amino acids with the condensation of two terminal amino acids of the linear peptide to form a cyclic compound. The cyclic nature of microcystins suggests that they are highly stable in water across a wide range of pH and temperatures. Microcystins are produced by several blue-green algae (cyanobacteria) including Microcystis, Anabaena, Planktothrix, Oscillatoria and Radiocystis commonly found in freshwater reservoirs in Ghana. Microcystins have very serious health implications on both humans and animals. Known symptoms associated with microcystin poisoning include skin irritation, allergic responses, mucosa blistering, muscular and joint pains, gastroenteritis, pulmonary consolidation, liver and kidney damage and other neurological effects. Methods: In this study, we present results of toxicological analysis conducted on water samples from the Brimsu and Kwanyarko Reservoirs used as sources of drinking water by some parts of the Central Region of Ghana in 2011. HPLC was used to measure microcystin and phytoplankton was identified using an inverted microscope. Results: HPLC analyses of samples gave four variants of microcystin, MC-LR, MC-YR, MC-RR and MC-LA with microcystins ranging from 0.79 µg/L during the intake of water at the Brimsu treatment plant to 0.1 µg/L in the final drinking water products of both reservoirs. Microcystin-LA is a microcystin variant identified in Ghana for the first time. Cyanobacteria diversity was low in both reservoirs. However, biomass was very high and constituted about 84% and 93% of the total algal counts of the water intake for Kwanyarko and Brimsu Reservoirs respectively. Dominant cyanobacteria species found in these reservoirs are Microcystis aeroginosa and Planktothrix agardhii. Conclusions: Due to the chronic effect of these toxins it is recommended that drinking reservoirs with low levels of microcystins must be regularly monitored to keep it free from microcystin to ensure safeguarding human health.