Autumn productivity is key to the large marine ecosystems of the Agulhas Bank, which support numerous economically important regional fisheries. Despite such importance, data is sparce on plankton composition in terms of primary or secondary producers, or on trophic transfer. While investigating autumn plankton composition we found that nanophytoplankton (2-20 µm) dominated carbon stocks, with lower contributions from picophytoplankton (<2 µm) and microphytoplankton (>20 µm). While picoplankton biomass exhibited a relationship with warm nutrient poor waters, nanoplankton showed no clear relationship to environmental parameters. The dominance of nanophytoplankton biomass on the Agulhas Bank highlights a critical role for micro-zooplankton grazing as a trophic transfer between these small plankton, meso-zooplankton and the higher trophic levels that make the bank so important for regional fisheries. Outside of localized coastal upwelling on the Agulhas Bank, this study highlights a significant role for nanoplankton and micro-zooplankton in supporting the bank’s large marine ecosystems.