Seismic profiling, bathymetric and physical oceanographic data collected from the Canakkale Strait revealed that the morphological evolution of the strait has been controlled by tectonic activity, and sediment erosion and deposition. Sediments in the strait have been sourced mostly by rivers draining the Biga Peninsula during lowstand periods. In highstand periods, by contrast, deposits in the strait were reworked by currents. The seafloor morphology of the Canakkale Strait is also controlled by a sequence of factors ranging from tectonics to current erosion and deposition. Channel deposits overlying the basement are being eroded at the narrower, meandering central section of the strait (the Nara Passage) due to high current velocities. The eroded sediments are deposited in the relatively linear and wider, northern and southern sectors of the strait exposed to low current velocities. As a result, the high-energy areas are more deeply incised due to the erosion, whereas deposition elevates the seafloor in the areas exposed to lower current energy. Three strike-slip faults, which possibly relate to the activity of the North Anatolian Fault Zone, are responsible for the irregular shape of the strait and this, in turn, controls the current velocity along the strait. The high-energy conditions probably commenced with the latest invasion of Mediterranean waters some 12 ka B.P., and have continued as a two-layered current system to the present day.