Processing and interpretation of a grid of intermediate-resolution multichannel seismic reflection profiles collected on the NE sector of the South Shetland continental margin, allowed us to map the lateral extent of a Bottom Simulating Reflector (BSR). The margin, an accretionary wedge located off the northern tip of the Antarctic Peninsula, consists of two distinct and superimposed tectonic regimes: an older regime is related to Mesozoic–Middle Cenozoic subduction-related tectonism; a younger one is associated with a mainly extensional tectonic phase, and related to the Oligocene development of the western Scotia Sea. The occurrence of the BSR appears to be controlled by the geological structure of the margin. The BSR lacks continuity near basement structures, main geological discontinuities and faults. On the other hand, the amplitude and continuity of the BSR are not affected by the presence of folded structures and undeformed sedimentary layering. We found that the BSR is mostly confined to the NE sector of the South Shetland Margin, where propagation of faulting associated with the Shackleton Fracture Zone may have driven migration of natural gas towards the surface and created the conditions for a BSR to appear. The application of reflection tomography techniques allowed us to reconstruct the averaged seismic velocity field between the seafloor and BSR in order to map the depth of BSR. By averaging the observed velocity structure above and below the BSR, and applying a theoretical model of elastic wave propagation in porous media, we attempted as rigorous a quantitative assessment as possible of the natural gas present as gas hydrate above the BSR and as free gas between the BSR and the Base of Gas Reflector (BGR).