The passage is underlain by a seismically active rift zone that overprints an older, partly eroded tilted-block structure.

The ridge forms the southern boundary of the 4-kilometer-deep (2.5 mi) Mona Canyon, which extends toward the north into the Puerto Rico Trench.

[4] Semidiurnal tidal currents impinging on a submarine ridge known as El Pichincho can force the generation of an internal tide with a wave height of 40 meters (130 ft).

[5] Underwater glider observations reveal wave damping as the internal tide propagates south along the Mona Passage towards the open Caribbean Sea.

The development of Kelvin-Helmholtz instability during the breaking of the internal tide can explain the formation of high-diffusivity patches that generate a vertical flux of nitrate (NO3−) into the photic zone and can sustain new production locally.