The Puerto Rico Trench is located on the boundary between the North Atlantic Ocean and Caribbean Sea, parallel to and north of Puerto Rico, where the oceanic trench reaches the deepest points in the Atlantic Ocean. The trench is associated with a complex transition from the Lesser Antilles frontal subduction zone between the South American plate and Caribbean plate to the oblique subduction zone and the strike-slip transform fault zone between the North American plate and Caribbean plate, which extends from the Puerto Rico Trench at the Puerto Rico–Virgin Islands microplate through the Cayman Trough at the Gonâve microplate to the Middle America Trench at the Cocos plate.

Constituting the deepest points in the Atlantic Ocean, the trench is 810 kilometres (503 mi) long and has a maximum documented depth between 8,376 metres (27,480 ft) and 8,740 metres (28,675 ft). The deepest point is commonly referred to as the Milwaukee Deep, with the Brownson Deep naming the seabed surrounding it. However, more recently, the latter term has also been used interchangeably with the former to refer to this point. The exact point was identified by the DSSV Pressure Drop using a state-of-the-art Kongsberg EM124 multibeam sonar in 2018, and then directly visited and its depth verified by the crewed submersible Deep-Submergence Vehicle DSV Limiting Factor (a Triton 36000/2 model submersible) piloted by Victor Vescovo.

Scientific studies have concluded that an earthquake occurring along this fault zone could generate a significant tsunami. The island of Puerto Rico, which lies immediately to the south of the fault zone and the trench, suffered a destructive tsunami soon after the 1918 San Fermín earthquake.

The Puerto Rico Trench is located at a boundary between two plates that pass each other along a transform boundary with only a small component of subduction. The Caribbean plate is moving to the east relative to the North American plate. The North American plate is being subducted by the Caribbean plate obliquely at the trench while to the southeast, the South American plate is being more directly subducted along the Lesser Antilles subduction zone. This subduction zone explains the presence of active volcanoes over the southeastern part of the Caribbean Sea. Volcanic activity is frequent along the Lesser Antilles island arc southeast from Puerto Rico to the northern coast of South America.

Although originally part of a volcanic arc, the Virgin Islands, Puerto Rico, Hispaniola, Cuba, and Jamaica do not have active volcanoes. The Virgin Islands and Puerto Rico do not have active volcanic activity since approximately 30 million years ago, while the last active volcanoes in Hispaniola, Thomazanue and Morne la Vigie, became extinct within 1.5 million years ago. However, the islands are at risk of earthquakes and tsunamis. The Puerto Rico Trench has produced earthquakes greater than magnitude 8.0 and is considered capable of continuing to do so.

According to NASA, beneath the trench is a mass so dense it deflects gravitational pull on the surface of the ocean, causing it to dip somewhat. It also has a negative effect on the accuracy of navigational instruments.

Knowledge of the earthquake and tsunami risks has not been widespread among the general public of the islands located near the trench. Since 1988, the Puerto Rican Seismic Society has been trying to use the Puerto Rican media to inform people about a future earthquake that could result in a catastrophic tragedy.

Following the 2004 tsunami that affected more than forty countries in the Indian Ocean, many more people now fear the consequences that such an event would bring to the Caribbean. Local governments have begun emergency planning. In the case of Puerto Rico and the U.S. Virgin Islands, the United States government has been studying the problem for years. It is increasing its seismic investigations and developing tsunami warning systems.