The Puerto Rican Operating Area, often inaccurately called the "Roosevelt Roads Operating Area", was centered on the Virgin Pass and Vieques. Because of Puerto Rican protests, it is now closed.

Vieques Island was the site of the former Vieques Naval Training Range which was primarily used to train surface combatants for Naval Surface Fire Support. This training consisted of shooting live rounds at specified targets inside the range, 9 to 13 miles from the nearest populated area.

Prompted by the accidental death of a civilian guard, David Sanes, inside the range, the people of Puerto Rico began a movement to close it. Environmental and health issues fueled the opposition of the people against keeping the range open. A nearby civilian area allegedly was adversely affected by the military operations. The opposition was mainly peaceful, relying on civil disobedience and massive protests. Nevertheless, some violent incidents did occur. A controversy arose because pro-independence and nationalist movements used the process to promote independence for Puerto Rico. However, with the protests and subsequent closing of the range, there was no longer any reason for Navy and Marine Corps forces to deploy to the Caribbean Sea, and the closing of Vieques' support base, U.S. Naval Station Roosevelt Roads, occurred on March 31, 2004. As a consequence, the U.S. Navy's more than $300 million in yearly economic impact, and thousands of military, federal and contractor jobs were lost on both Vieques Island, Puerto Rico and the Virgin Islands.