The combination of concentrations and δ¹³C signatures of Particulate Organic Carbon (POC) and sterols provides a powerful approach to study ecological and environmental changes both in the modern and ancient ocean, but its application has so far been restricted to the surface area. We applied this tool to study the biogeochemical changes in the modern ocean water column during the BONUS-GoodHope survey (Feb-Mar 2008) from Cape Basin to the northern part of the Weddell Gyre. Cholesterol and brassicasterol were chosen as ideal biomarkers of the heterotrophic and autotrophic carbon pools, respectively, because of their ubiquitous and relatively refractory nature. We document depth distributions of concentrations (relative to bulk POC) and δ¹³C signatures of cholesterol and brassicasterol from the Cape Basin to the northern Weddell Gyre combined with CO₂ aq. surface concentration variation. While relationships between surface water CO₂ aq. and δ¹³C of bulk POC and biomarkers have been previously established for surface waters, our data show that these remain valid in deeper waters, suggesting that δ¹³C signatures of certain biomarkers could be developed as proxies for surface water CO₂ aq. Our data suggest a key role of zooplankton fecal aggregates in carbon export for this part of the Southern Ocean. We observed a general increase in sterol δ¹³C signatures with depth, which is likely related to a combination of particle size effects, selective feeding on larger cells by zooplankton, and growth rate related effects Additionally, in the southern part of the transect south of the Polar Front (PF), the release of sea-ice algae is hypothesized to influence the isotopic signature of sterols in the open ocean. Overall, combined use of δ¹³C and concentrations measurements of both bulk organic C and specific sterol markers throughout the water column shows the promising potential of analyzing δ¹³C signatures of individual marine sterols to explore the recent history of plankton and the fate of organic matter in the SO.