The stable isotopic composition of particulate organic carbon (δ13CPOC) in the surface waters of the global ocean can vary with the aqueous CO2 concentration ([CO2(aq)]) and affects the trophic transfer of carbon isotopes in the marine food web. Other factors such as cell size, growth rate and carbon concentrating mechanisms decouple this observed correlation. Here, the variability in δ13CPOC is investigated in surface waters across the south subtropical convergence (SSTC) in the Atlantic Ocean, to determine carbon isotope fractionation (εp) by phytoplankton and the contrasting mechanisms of carbon uptake in the subantarctic and subtropical water masses. Our results indicate that cell size is the primary determinant of δ13CPOC across the Atlantic SSTC in summer. Combining cell size estimates with CO2 concentrations, we can accurately estimate εp within the varying surface water masses in this region. We further utilize these results to investigate future changes in εp with increased anthropogenic carbon availability. Our results suggest that smaller cells, which are prevalent in the subtropical ocean, will respond less to increased [CO2(aq)] than the larger cells found south of the SSTC and in the wider Southern Ocean. In the subantarctic water masses, isotopic fractionation during carbon uptake will likely increase, both with increasing CO2 availability to the cell, but also if increased stratification leads to decreases in average community cell size. Coupled with decreasing δ13C of [CO2(aq)] due to anthropogenic CO2 emissions, this change in isotopic fractionation and lowering of δ13CPOC may propagate through the marine food web, with implications for the use of δ13CPOC as a tracer of dietary sources in the marine environment.