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We use ambient noise records obtained by a vertical array of seismometers at borehole and seafloor in the Kumano basin of the Nankai subduction zone, Japan, and examine whether S reflections from deep interfaces can be persistently detected or not. The vertical array contains a geophone at the seafloor and a borehole broadband sensor at a depth of 900 m from the seafloor. Our results show the retrieval of S reflections from the top of high velocity body above the megasplay fault, the megasplay fault itself, and the top of the subducting oceanic crust. The depths of these boundaries are 5–10 km from the sea surface. The arrival time of the S reflection for a polarization direction of N70ºE was faster, indicating that the direction is the fast polarization direction. We also investigated the temporal variation of the amplitudes of the S reflections at a slow polarization direction (N160ºE), and obtained temporal variations in amplitudes of the S reflections from the top of the high velocity body and megasplay fault for 1 year after 2016 off-Mie earthquake (Mw5.9) whose epicenter is ~30 km away from the vertical array. This may be related to fluid migration around these boundaries.