Abstract. The accumulation of anthropogenic CO2 emissions in the atmosphere has been buffered by the absorption of CO2 by the global ocean, which acts as a net CO2 sink. The CO2 flux between the atmosphere and the ocean, which collectively results in the oceanic carbon sink, is spatially and temporally variable, and fully understanding the driving mechanisms behind this flux is key to assessing how the sink may change in the future. In this study a time series decomposition analysis was applied to satellite observations to determine the drivers that control the sea–air difference of CO2 partial pressure (ΔpCO2) and the CO2 flux on seasonal and inter-annual timescales in the South Atlantic Ocean. Linear trends in ΔpCO2 and the CO2 flux were calculated to identify key areas of change. Seasonally, changes in both the ΔpCO2 and CO2 flux were dominated by sea surface temperature (SST) in the subtropics (north of 40∘ S) and were correlated with biological processes in the subpolar regions (south of 40∘ S). In the equatorial Atlantic, analysis of the data indicated that biological processes are likely a key driver as a response to upwelling and riverine inputs. These results highlighted that seasonally ΔpCO2 can act as an indicator to identify drivers of the CO2 flux. Inter-annually, the SST and biological contributions to the CO2 flux in the subtropics were correlated with the multivariate El Niño–Southern Oscillation (ENSO) index (MEI), which leads to a weaker (stronger) CO2 sink in El Niño (La Niña) years. The 16-year time series identified significant trends in ΔpCO2 and CO2 flux; however, these trends were not always consistent in spatial extent. Therefore, predicting the oceanic response to climate change requires the examination of CO2 flux rather than ΔpCO2. Positive CO2 flux trends (weakening sink for atmospheric CO2) were identified within the Benguela upwelling system, consistent with increased upwelling and wind speeds. Negative trends in the CO2 flux (intensifying sink for atmospheric CO2) offshore into the South Atlantic gyre were consistent with an increase in the export of nutrients from mesoscale features, which drives the biological drawdown of CO2. These multi-year trends in the CO2 flux indicate that the biological contribution to changes in the air–sea CO2 flux cannot be overlooked when scaling up to estimates of the global ocean carbon sink.