Hurricane Maria, a Category Five storm, passed over Puerto Rico and the Virgin Islands on 21 September. 15 people were killed in Puerto Rico and the storm left the entire island without power. It was described as the most devastating storm the territory has experienced in a hundred years.

Maria had briefly weakened to Category 4 after devastating Dominica, but since regained strength. Over 12,000 people took refuge in 500 emergency shelters in advance of the storm in Puerto Rico, which left widespread flooding over half a metre deep in some locations. Many homes, particularly those constructed with wood, were flattened by Maria's strong winds or inundated in the resulting floods. There are concerns that it may take months to restore power to the island, such was the damage to the island's power grid.

The storm left many stranded by floods, and almost crippled the communications network, making relief efforts and assessments of the damage difficult. Estimates suggest San Juan, on the coast, has particularly suffered, with 80% of homes suffering at least some damage.

The island is still housing evacuees from other nearby Caribbean islands that were affected by Hurricane Irma, which narrowly avoided Puerto Rico.

In the U.S. Virgin Islands one person was killed as the storm passed close by, particularly affecting the island of St. Croix.