As with the ancient accretionary prism formed in the Southern Uplands during the Caledonian orogeny, the Nankai accretionary prism is a product of the tectonic processes at collision plate margins. The Nankai trough marks the subduction of the Philippine Sea plate beneath Japan, part of the Eurasian plate. This type of plate boundary is usually in the form of an Oceanic trench (as with other boundaries at the edge of the Pacific Plate), but at this site a high volume of sediments accumulating in the Nankai trough means that there is a substantial amount of deformed trench sediments. There are also a number of seamounts (submarine mountains) rising from the sea floor in this area that are covered in the accumulating sediments.

	Longitudinal section through an underwater turbidity current: © NOAA

The deposits found in the accretionary prism are predominantly turbidites, sediments deposited by sediment-laden downhill flows of water that are common in trough environments. Turbidity currents can be thought of as underwater avalanches which travel down the steep slopes of the continental shelf and deposit sediments on the sea floor in order from coarse to fine as the current travels away from the slope. This sequence of deposition creates the characteristic Bouma sequence.

The fault that underlies the submarine trough, the Nankai megathrust, is the source of the often devastating megathrust earthquakes experienced in this region of Japan. The trough is a region of very active deformation and seismic activity and several thrust faults have been identified throughout. Recently the International Ocean Discovery Programme completed an expedition to drill cores in the Nankai trough to observe the sub-seafloor biosphere in the accretionary prism.