Between 1901 and 1975, the U.S. military used Culebra and adjacent islands and cays. Initially, it was used as a coaling station and a radio transmitter facility. Eventually the U.S. Navy established areas for naval gun firing and aerial bombing. The U.S. Marines held advanced base defense exercises on the island that included land maneuvers, artillery and small arms firing, and amphibious training. The military stopped firing on Culebra in 1975, but munitions may still on the island and in the water.

The U.S. Army Corps of Engineers manages the Defense Environmental Restoration Program for Formerly Used Defense Sites (FUDS) on behalf of the Department of Defense. All of the island of Culebra, Culebrita, Cayo Luis Peña, Cayo Norte, other nearby cays and the surrounding waters are within the Formerly Used Defense Site. The U.S. Army Corps of Engineers divided the site into 15 project areas. One of those is an area where metallic debris may have been discarded. In the other 14 areas, known as Munitions Response Sites (MRS), the Corps is concerned that there may be military munitions present.

 The entire Northwest Peninsula of Culebra was used for naval shore and aerial bombardment. The land, including Flamenco Beach, was transferred by deed to the Commonwealth of Puerto Rico, which is responsible for restoration, including removing munitions. In response to a congressional request, the U.S. Army Corps of Engineers studied the part of the Northwest Peninsula the Commonwealth owns to determine the type and amount of munitions remaining. The Secretary of the Army received authorization from Congress to remove unexploded ordnance certain public use areas within the Northwest Peninsula under Section 317 of Public Law 113-291 in December 2014. These areas include portions of Carlos Rosario Beach, Flamenco Beach, Tamarindo Beach, the Flamenco campground, and Carlos Rosario Trail. The remaining acreage not covered by these areas remains the responsibility of the Commonwealth of Puerto Rico to restrict access and/or provide remediation. 

In May 2016, the U.S. Army Corps of Engineers received authorization to conduct a Time Critical Removal Action at the Congressionally Authorized Areas within the Northwest Peninsula. The contract for the Time Critical Removal Action was awarded in June 2016, and fieldwork was underway when Hurricane Irma formed in the Caribbean.  The contractor teams left the island, and before they could return, Hurricane María further damaged Culebra.  After obtaining concurrence from the Culebra mayor's office and the Authority for the Conservation and Development of Culebra, the Corps' contractor remobilized and resumed operations in November 2017.  The contractor brought in additional teams to expedite fieldwork to complete intrusive activities prior to spring break and Holy Week.  In March 2018, all fieldwork operations were completed.  The Corps anticipates that the final report concerning the Time Critical Removal Action will be completed in early Fiscal Year 2019.

In addition, the U.S. Army Corps of Engineers received authorization to conduct Time Critical Removal Actions at Cayo del Agua and Cayo Botella in June 2016. The fieldwork at Cayo Botella and Cayo del Agua are scheduled for completion in Fiscal Year 2019, with a final report on both projects in early Fiscal Year 2020.