Toxic freshwater cyanobacterial blooms are potential health hazards in water supply reservoirs and therefore predicting bloom events is an important goal of monitoring fresh water programmes. The recent identification of the mcy genes in the production of microcystin synthetase for the first time provides an avenue to study microcystin production at a genetic level. This paper reports analysis of a winter cyanobacterial bloom by use of quantitative real-time PCR, ELISA and PP2A methods for detection of strains present and determination of their toxigenicity in Lake Midmar South Africa. We further investigated the taxonomic composition of phytoplankton at different sampling sites and the physical and chemical changes caused in the surface water of Lake Midmar by waterfowl. Our study clearly demonstrates that the interaction between low surface water temperatures and productivity was overshadowed by the response to nutrients and nutrient availability. We also confirmed the presence of the toxic cyanobacterial strains through the use of molecular markers that detect the presence of some of the mcy genes in the mcy gene cluster that is able to synthesize microcystin toxins in Microcystis spp.