Huge populations of sardine and anchovy exist in the four major upwelling systems around the world. These fish are both important ecologically and economically. Pelagic fish dominate the mid trophic level and can exert both a top-down control of zooplankton and a bottom-up control on predatory fish and marine top predators. They also make up a substantial contribution of the world catches in seas around the world where they co-exist in upwelling areas. The fluctuations of sardine and anchovy are largely influenced by recruitment from the larval stage and by the physical environmental forces that determine the planktonic compositions upon which they feed. In southern Africa, the biology and behaviour of two threatened seabird species, African penguins (Spheniscus demersus) and Cape gannets (Morus capensis), are directly influenced by the availability of sardine (Sardinops sagax) and anchovy (Engraulis encrasicolus). This study aimed to provide further insight into the fluctuations of sardine and anchovy in relation to the variability of environmental factors such as wind, sea surface temperature, rainfall and plankton abundance, focusing specifically on Algoa Bay in the Eastern Cape, South Africa. Algoa Bay is particularly important as it is home to the world’s largest African penguin colony and the world’s largest gannetry. Therefore, to further investigate the populations of these two seabird species, the fluctuations of their food source were studied.