Processes governing productivity at the base of the pelagic food web of the southern Indian Ocean are influenced primarily by physical–chemical conditions with implications for the structure and function of the entire pelagic food web. Here, we report observations along a great circle transect from Cape Town, South Africa, to Broome in north western Australia. Primary production was tightly linked to water column stability and nutrient availability, with high productivity (1144 mg C m−2 day−1) in the sub-tropical convergence zone, and falling off by an order of magnitude in the sub-tropical gyre and tropical waters off northwest Australia. Primary production was largely confined to the GF/F fraction (GF/F >75% of total production and usually much higher) and the photosynthetic parameters showed adaption to the prevailing light levels. Bacterial production ranged from 19 to 155 mg C m−2 day−1. No relationships were found between bacterial production and primary production or phytoplankton biomass and bacterial production seem more related to the state of the phytoplankton community as high bacterial production was observed in a post-bloom situation. The average BP:PP ratio was 31% (range 3.5–71%).