Paleo-ocean circulation models of the Southern Ocean suffer from missing boundary conditions which describe accurately the geometries of the seafloor surfaces at their geological epoch and their dynamics over long time-scales. The accurate parameterisation of these models controls the meaning and implications of regional and global paleo-climate models. For instance, the onset and consequences of the deep-water opening of the Southern Ocean gateways – Drake Passage and the Tasmanian Gateway – is only indirectly and vaguely determined by proxy analyses of microfossils. The development and implications for deflections of major deep-sea current systems through structural obstacles such as oceanic plateaus and ridges, but also the extent and morphological shape of the continental shelves, is not described due to lacking reconstructions of their bathymetric development. Although plate-kinematic reconstructions of the Southern Ocean have reached a state at which the plate circuit can be almost closed with geodynamic constraints of improving certainties, a major obstacle for calculating Southern Ocean paleobathymetric grids has been the missing or insufficiently assessed components of sedimentary deposition/erosion and mantle-driven dynamic topography. Existing paleobathymetric models consider only the top of oceanic basement based on paleo-age models from magnetic sea-floor spreading anomalies and plate-kinematic reconstructions. Others simplify the sedimentary cover using outdated isopach databases. A re-assessment of old seismic data as well as recently collected new seismic lines reveal that the sedimentary cover has been greatly underestimated in almost all conjugate continental margins and in some of the deep Southern Ocean basins. Incorporating sedimentary processes in paleobathymetric reconstruction grids is particularly important in reconstructing the opening of oceanic gateways where the question of shallow to deep water exchange determines the accuracy of paleo-ocean circulation and paleo-climate models. But also the dynamics of ocean currents in proximity of the continental margins is controlled by the development of the regional morphology of the conjugate continental shelves, slopes and rises. The ultimate aim of such grids is to generate Cenozoic climate reconstructions using a variety of Earth system models designed to evaluate the effect of ocean gateways and basins on paleo-circulation patterns, the global carbon cycle and the nature of Antarctic ice sheet development. These experiments will include sensitivity runs incorporating the new paleobathymetric reconstructions. The results from these experiments are compared with other model simulations, which include different forcing factors such as atmospheric greenhouse gasses and mountain uplift to determine the relative importance of paleo-geography on the evolution of global climates over long geological timescales.