New bathymetric and subsurface data from the Santos Basin, offshore southeast Brazil, reveal sharp lateral morphological variations facing the margin-parallel (along-margin) flow of the Antarctic Intermediate Water. The data, derived from 3D Pre-Stack Depth Migrated (PSDM) seismic reflection volumes, show on a ~100 km long Southern segment slope gullies, mass transport deposits, and scars. These morphologies sharply shift laterally to a ~50 km long Northern segment, typified by a smooth relief built of plastered contourite drifts with occasional elongated depressions. We examine this sharp lateral shift in the morphology of bottom current indicators in view of the hydrodynamical regime, sediment sources, and their distribution pattern. Results indicate that the sharp lateral morphological shift is attributed to (1) a 30◦ change in slope orientation, and (2) a northward increase in the across-margin velocity component of the Intermediate Water Boundary Current (IWBC). Subsurface data suggest this flow pattern has persisted since the mid-Miocene. In this case study, the lateral morphological shifts under contemporary hydrodynamic conditions emphasize the importance of understanding the coupling between ocean bottom currents and the seafloor in any marine environment.