Quantifying greenhouse gas (GHG) emissions is essential for mitigating global warming, and has become the task of individual countries assigned to the Paris agreement in the form of National Greenhouse Gas Inventory Reports (NIR). The NIR informs on GHG emissions and removals over national territory encompassing the 200-mile Exclusive Economic Zone (EEZ). However, apart from only a few countries, who have begun to report on coastal ecosystems, mostly mangroves, salt marshes, and seagrass meadows, the NIR does not cover or report on GHG sources and sinks of the 200-mile exclusive economic zone which, for Namibia and South Africa includes the Benguela Upwelling System (BUS). Based on our results, we estimated a CO2 uptake by the biological carbon pump of 18.5 ± 3.3 Tg C year−1 and 6.0 ± 5.0 Tg C year−1 for the Namibian and South African parts of the BUS, respectively. Even though it is assumed that the biological carbon pump already responds to global change and fisheries, uncertainties associated with estimates of the CO2 uptake by the biological carbon pump are still large and hamper a thorough quantification of human impacts on the biological carbon pump. Despite these uncertainties, it is suggested to include parameters such as preformed nutrient supply, carbon export rates, Redfield ratios, and CO2 concentrations measured at specific key sites into the NIR to stay focussed on the biological carbon pump and to support research addressing open questions, as well as to improve methods and observing concepts.