Although there are many research studies on the northern and southern branches of the North Anatolian fault, cutting through the deep basins of the Sea of Marmara in the north and creating a series of pull-apart basins on the southern mainland, little data is available about the geometrical and kinematical characteristics of the middle strand of the North Anatolian fault. The first detailed geometry of the middle strand of the North Anatolian fault along the southern Marmara shelf, including the Gemlik and Bandirma Bay, will be given in this study, by a combined interpretation of different seismic data sets. The characteristic features of its segments and their importance on the paleogeographic evolution of the southern shelf sub-basins were defined. The longest one of these faults, the Armutlu-Bandirma segment, is a 75-km long dextral strike-slip fault which connects the W-E trending Gencali segment in the east and NE-SW trending Kapidag-Edincik segment in the west. In this context, the Gemlik Bay opened as a pull-apart basin under the control of the middle strand whilst a new fault segment developed during the late Pleistocene, cutting through the eastern rim of the bay. In this region, a delta front forming the paleoshoreline of the Gemlik paleolake was cut and shifted approximately 60 +/- 5 m by the new segment. The same offset on this fault was also measured on a natural scarp of acoustic basement to the west and integrated with this paleoshoreline forming the slightly descending topset-foreset reflections of the delta front. Therefore the new segment is believed to be active at least for the last 30,000 years. The annual lateral slip rate representing this period of time will be 2 mm, which is quite consistent with modern GPS measurements. Towards the west, the Bandirma Bay is a rectangular transpressional basin whilst the Erdek Bay is a passive basin under the control of NW-SE trending faults. When the water level of the paleo-Marmara lake dropped down to -90 m, the water levels of the suspended paleolakes of Bandirma and Gemlik on the southern shelf were -50.3 (-3.3 Global Isostatic Adjustment-GIA) and -60.5 (-3.3 GIA) m below the present mean sea level, respectively. As of today a similar example can be seen between the Sea of Marmara and the shallow freshwater lakes of Manyas and Uluabat. Similarly, the paleolakes of Gemlik and Bandirma were affected by the water level fluctuations at different time periods, even though both lakes were isolated from the Sea of Marmara during the glacial periods.