Submarine Squadron 16 was established during World War II, and amassed more than 500,000 tons of enemy shipping sunk, earning both the Presidential Unit Citation and six Navy Unit Commendations before being decommissioned after the war. The squadron was formally recommissioned at Charleston, S.C., on Oct. 18, 1963, as the Navy's second Fleet Ballistic Missile (FBM) Submarine Squadron.

The Chief of Naval Operations deployed Submarine Squadron 16 to Rota, Spain, on Jan. 28, 1964, and embarked upon USS Proteus (AS-19). USS Lafayette (SSBN 616) completed its first FBM deterrent patrol with the Polaris missile and commenced the first refit and replenishment at Rota. During the early 1970s, the submarines assigned to Squadron 16 were completing conversion to the Poseidon missile. That transition was completed when USS Francis Scott Key (SSBN 657) returned to Rota on Jan. 14, 1974.

Treaty negotiations between Spain and the United States in 1975 resulted in a planned withdrawal of Squadron 16 from Spain, and the Chief of Naval Operations ordered studies to select a new refit site on the East Coast. The treaty with Spain was ratified by the U.S. Congress in June 1976 and called for the withdrawal of the squadron from Spain by July 1979. Kings Bay, Georgia, was selected as that new refit site, and the site selected was announced by the Secretary of the Navy in November 1976.