In this study we made a comparative interpretation of multibeam bathymetric and seismic reflection data with different resolutions and penetration properties collected in the Central Basin of the Marmara Sea. Our main objectives were (i) to investigate and compare the active tectonic deformation observed on the sea bottom and within the uppermost sedimentary layers to that of the deep-seated deformation within the limits of resolution and penetration of the available geophysical data and (ii) to build a three-dimensional (3D) block diagram of the active tectonic and buried features by means of a sliced mapping technique. In this approach, we produced slice maps of the active and buried structural features at selected depths and then combined them to form a 3D structural block diagram. Motivation for our work was to produce a 3D structural diagram to derive a more detailed image of the structural features in the Central Basin where there is no available 3D seismic data. The observations from the bathymetry and seismic data and developed 3D diagram support the presence of a through-going strike-slip fault that forms a rotational depression zone against a right-stepping strike-slip faulting causing a pull-apart basin in the Central Depression zone.