Harmful cyanobacterial blooms are of increasing global concern and their prediction and management requires an improved understanding of the controlling factors for cyanobacterial growth and dominance. In Lake St Charles, the drinking water supply for Quebec City, Canada, harmful cyanobacterial blooms were first recorded in autumn 2006. Our aims were to define the temporal and spatial variations in the cyanobacterial community structure of this reservoir and to address the hypothesis that interannual variability in cyanobacterial biomass and species composition is mainly controlled by nutrients, temperature and water column stratification. Over five consecutive summers (2007–2011), the north basin had consistently higher concentrations of bloom-forming cyanobacteria than the south basin, and there were striking variations within and among years in total biomass and species composition. Correlation analysis underscored the contrasting environmental controls on different taxa of colonial cyanobacteria. Anabaena flos-aquae biovolume was correlated with surface temperature, water column stability (Schmidt index) and water residence time whereas Microcystis aeruginosa was highly correlated with total phosphorus and to a lesser extent with total nitrogen (TN), heat accumulation (degree-days above 20°C) and precipitation. Aphanocapsa/Aphanothece correlated significantly only with TN. These results also imply the sensitivity of high through-flow reservoir ecosystems to interannual variations in environmental forcing.