We studied the active deformation zone of the middle strand of the North Anatolian Fault Zone through the southern part of the Sea of Marmara by means of high-resolution as well as deep seismic reflection data. Our main objective was to investigate the active deformation within the uppermost sedimentary layers at high resolution as well as deeper sedimentary layers, focusing on the tectonic and stratigraphic setting between Gemlik and Bandirma. The middle strand of the North Anatolian Fault reaching the Gulf of Gemlik is a main fault which has a lazy-S shape in the Gulf of Gemlik, and extends westwards to Bandirma as a main fault which is an E-W-trending single right-lateral fault controlling the zone along the Gemlik and Bandirma sub-basins. Small-scale faults, consistent with a dextral shear regime, are present in the vicinity of the main fault. Several oblique fault groups parallel to the main fault were detected. The deformation in the Gulf of Gemlik is characterized by a series of synthetic and antithetic faults emanating from the main fault. The boundary faults in the Gulf of Gemlik have a compressive component, which indicates the sill areas of the gulfs of Gemlik and Bandirma to be push-up structures. Four seismic stratigraphic units were identified in the sediments of the gulfs of Gemlik and Bandirma, providing evidence of tectonic influence. The present tectonic structure between Gemlik and Bandirma is not a pull-apart structure. The microseismic study in this area has shown that fault planes are either strike-slip or compressional, and that the stress tensor is compatible with pure strike-slip in the E-W fault system.