An index of upwelling and temperature profiles (indicating the dynamics of the upper mixed layer) gave a good qualitative prediction of the dominance of either small (4–10 µm) or intermediate-to-large (10–74 µm) phytoplankton cells in surface waters of St Helena Bay, a semi-enclosed bay in the Southern Benguela upwelling region on the west coast of South Africa. Phytoplankton cell size was determined with particle volume estimates obtained with a Coulter Counter. Predictions were made using a decision tree incorporating size-based theory and requiring wind and temperature data. Overall, the dominant phytoplankton cell size was correctly predicted 84% of the time. Successful prediction was higher in winter than in summer and higher for water offshore of the upwelling front. The transport of phytoplankton cells from adjacent water masses, variable re-seeding mechanisms and undetected non-phytoplankton cells hampered the achievement of full prediction success. The results of this study are of relevance to the assessment of the monthly feeding habitat available to zooplankton and juveniles of small pelagic fish, and a step towards understanding the trophic functioning of the Southern Benguela at the sub-annual scale.