Dense water out of the Antarctic shelves is expected to drive the transport of carbon into the deep Southern Ocean via the formation of Antarctic Bottom Water. However, bottom water formation’s capacity to sequester carbon into the deep ocean is poorly constrained. Here, dissolved organic carbon (DOC), dissolved black carbon (DBC), and particulate organic carbon (POC) were examined to reveal the influence of the Weddell Sea Deep Water (WSDW) on DOC transport during its flowing out of the Weddell Sea. High DOC concentrations (>60 μM-C) and low DBC/DOC ratios (<1.5%) were observed in surface water near the South Orkney Islands, ascribing to sea ice melt-induced phytoplankton blooms. Seawater at the mid-deep depths exhibited a higher DOC concentration (averaging 48.1 ± 3.7 μM-C) than the incoming water source, resulting from the release of DOC from sinking particles. Bottom water had higher DOC concentration compared to the mid-deep layer water (t-test, p < 0.005), while the DBC concentrations were comparable. In addition, the excess DOC (relative to WSDW) in bottom water showed a close relation with POC in surface water. These results reveal a top-down control over the DOC concentration in bottom water through a quick sinking of diatom detritus and subsequently solubilization in bottom water and/or sediment. With an estimate, the WSDW carries 5.1 ± 2.8 Tg-C/yr of excess DOC out of the Powell Basin, representing an important carbon source to the deep Southern Ocean. This study highlights the key role of the Antarctic continental shelf pump in carbon sequestration.