The Chief of Naval Operations deployed Submarine Squadron 16 (SUBRON 16) to Rota on 28 January 1964 and embarked upon USS Proteus.

In November 1976 the Secretary of the Navy announced Naval Submarine Base Kings Bay, Georgia as that new refit site.

Data was then forwarded to United States Sixth Fleet Headquarters, providing also critical intelligence regarding Soviet ships acoustic signatures, operating characteristics, and warfighting capabilities.

[2] As the U.S. Navy started to reduce its presence, the USAF realized the potential of the airfield as a refueling stop in Middle East deployments.

During that war B-52 Stratofortress bombers were stationed at nearby Morón Air Base, where detachements of USAF KC-135 Stratotanker aerial refueling aircraft had rotated during years.

Rear Admiral Tony Gaiani relieved Mosk for "lost confidence in his ability to command", specifically, to handle issues related to the investigation.

[14] Naval Station Rota is strategically located near the Strait of Gibraltar and at the halfway point between the United States and Southwest Asia.

The US Navy has the responsibility for maintaining the station's infrastructure, including a 670-acre (2.7 km2) airfield, three active piers, 426 facilities and 806 family housing units.

[clarification needed] Pest management is performed by a combination of Navy personnel, and local contractors who must be licensed by the host country (Spain).

As a result, certain US military customs are not observed, such as the display of a US Flag, which is only allowed during the annual Fourth of July celebration or occasionally at half mast as a mark of respect with the ad-hoc permission of the Spanish Admiral.

Rota supports Amphibious Readiness Group turnovers and hosts Sailors and Marines from visiting afloat units.

[2] The Operational Headquarters (OHQ) for the EU Naval Force moved from Northwood, UK to Rota and to Brest, France on 29 March 2019.