This study examined phytoplankton communities in Algoa Bay, South Africa at different temporal scales. A time-series from 2010-2012 showed strong seasonal variability in sea surface temperature, with cooler temperatures and higher chlorophyll-a in 2010/2011 and warmer temperatures and lower chlorophyll-a in 2011/2012. This corresponded to dominance of south-easterly winds in 2010/2011 which cooled waters and increased phytoplankton biomass. Sampling trips found dinoflagellates dominant in early summer 2011 and pennate diatoms dominant in early autumn 2012, corresponding to nutrient levels and water column mixing at the time.