Entering the northeastern Caribbean Sea, rapid intensification ensued and it peaked on September 16 north of Puerto Rico as a Category 3 hurricane shortly after it had impacted the U.S. Virgin Islands.

Eleven thousand people were left homeless on the island of St. Thomas, and estimated damages were set at $2 billion (1995 USD)[1] in the USVI.

On September 12, satellite pictures viewed the disorganized wave and declared it Tropical Depression Fifteen, after convection had increased.

[3] Marilyn passed over Dominica, and just Îles des Saintes and southwest of Guadeloupe on September 14, bringing heavy rains and strong winds with it.

Marilyn continued on its northwesterly track, making landfall in the U.S. Virgin Islands on September 15, packing winds of 110 mph (180 km/h), a strong Category 2 strength hurricane.

An eye formed in the center of Marilyn, and the storm reached a peak intensity of 949 millibars and winds of 115 mph (185 km/h), a lower-end Category 3 hurricane.

This rapid weakening was caused by westerly shear and dry air entrained in the system, a decaying eyewall, and especially cool waters upwelled from the previous powerful storm, Hurricane Luis.

As Marilyn weakened to Category 1 hurricane status and moved north-northwest, it passed about 174 mi (280 km) west of Bermuda on September 19.

As Marilyn encountered more westerly shear, it weakened to below hurricane status and made its extratropical transition on September 20, centered in the northeastern Atlantic.

[3] The remnant circulation continued to erratically move through the central Atlantic Ocean for another 10 days before being absorbed by a frontal low on September 30.

A tropical storm warning was issued for St. Lucia, St. Vincent, Grenadines, Grenada and Tobago at 900 UTC September 13.

Four hours later, Puerto Rico, U.S. and British Virgin Islands, and Guadeloupe were put under a hurricane warning.

At 1500 UTC September 15, Dominican Republic from Cabrera to Cabo Engano were put under a hurricane watch as Marilyn approached.

At around the same time, a new Hurricane watch was released for Turks and Caicos and Mayaguana, Acklins, and the Crooked Islands of the southeastern Bahamas.

Aside from high winds and seas, one possible explanation for the storm's heavy damage may have been complacency on the part of local island populations.

Marilyn struck a mere 10‑days after Luis, a more powerful Category 4 hurricane initially predicted to pass very close to St. Thomas.

This prediction prompted locals to be particularly thorough in their pre-storm preparations; however, Luis passed further away from the island and caused relatively moderate damage.

Marilyn was one of the three hurricanes that affected the region in 1995, after Iris and Luis; the total estimated damage was near 500 million francs.

[3] The island of St. Thomas was the hardest hit by the storm, where about 80% of the homes and businesses were damaged or destroyed, including the hospital and the water desalination plant; five people were killed.

Storm surge in the Charlotte Amalie harbor beached the USCGC Point Ledge and damaged many smaller boats.

There were reports of extensive flash flooding across northern and eastern Puerto Rico, and 12,000 people were forced to ride out the storm in shelters.

[31] Five supply distribution sites were being operated by the Virgin Islands Territorial Emergency Management Agency (VITEMA).

Diving teams were sent to check for harbor damage and United States Navy Seabees started working on repairing public buildings.

[35] Due to the destruction caused by the hurricane, the name Marilyn was retired in the spring of 1996 by the World Meteorological Organization, and will never again be used for a North Atlantic tropical storm.