The atmospheric CO2 content has been discussed as one of the major factors influencing global climate. In the framework of the deep ocean forming the main reservoir of carbon dioxide, the Southern Ocean plays a crucial role in partitioning carbon between the atmosphere and the deep ocean. The processes resulting in the variability of atmospheric CO2 and carbon uptake in the deep ocean have not yet been fully identified. Sedimentary structures imaged with seismic reflection data in Princess Elizabeth Trough, the deep water gateway between the Kerguelen Plateau and Prydz Bay, are interpreted regarding direction and intensity of pathways of deep/bottom water masses transported in gyres, eddies, and boundary currents to contribute to the knowledge on potential locations of carbon subsidence. Under the assumption that the general circulation scheme has been similar during the Neogene, i.e., driven by gyres, the positions and sizes of palaeo-gyres have been reconstructed, which, combined with information from ODP Leg 188 Sites 1165 and 1167, were then interpreted regarding the potential intensity of carbon uptake. This has been compared with published reconstructions of warming/cooling trends of the global climate. While the method applied is equivocal, it links observed sedimentary structures with the development of gyres, thus potential locations of carbon uptake. This way the presented reconstruction provides pieces to the climate variability puzzle, which can be tested using numerical simulation.