We investigated Gemlik Bay of the Marmara Sea with an extensive high-resolution shallow seismic survey to locate and map active traces of the southern strand of the North Anatolian Fault (NAF). The southern strand splits from the main trace of the North Anatolian Fault about 80 km southeast of İzmit and extends as a continuous trace to the west for about 140 km to Gemlik Bay where it enters the Sea of Marmara. The seismic profiles reveal many faults that offset the Quaternary deposits. We interpret that four major fault zones play a significant role in shaping Gemlik Bay, the Gemlik, Kocadere–Mudanya, Gençali and Armutlu Faults, and propose that these faults are responsible for the formation of two prominent morphological features in the bay, namely Burgaz Depression and Gemlik Rise which are a pull-apart basin and a push-up structure, respectively. Closely spaced profiles to interpret the fault patterns and complex kinematics, therefore, are shown to be necessary in such areas. Besides active fault traces along the profiles, we also observed mass movements along the southern shore, offshore Mudanya–Zeytinbağı and Kurşunlu in the study area. Although no destructive earthquakes were experienced in the region recently the mass movements observed on the seafloor indicate remarkable past activity along the southern strand of the North Anatolian Fault which is overshadowed by the northern strand in 20th century from seismicity point of view.