Archaeological research has revealed a pre-Columbian era Indian presence throughout the area, dating back thousands of years.

Early in the 19th century, much of what is now the submarine base was the site of several plantations, including Cherry Point, Harmony Hall, New Canaan, Marianna and Kings Bay.

John Houston McIntosh built a considerably larger plantation known as New Canaan, where he grew cotton and sugar cane.

Such residents harvested shrimp, fish and other seafood, and trapped and hunted to supplement small-scale farming of corn, sugar and other vegetables.

The US Army began to acquire 7,000 acres (28.33 km2; 10.94 sq mi) of land at Kings Bay in 1954 to build a military ocean terminal to ship ammunition in case of a national emergency.

These mounds of dirt, still prominent features in many areas of the base, were designed to localize damage in case of explosive accidents.

It was soon realized that there was no immediate operational need for the installation, so it was placed in an inactive ready status, and Blue Star Shipping Company signed a lease to use the wharf in 1959.

Also, during the Cuban Missile Crisis, an Army Transportation Battalion of 1,100 personnel and 70 small boats took up position at Kings Bay.

A proposed change to the United States naval basing agreement with Spain included the withdrawal of the fleet ballistic-missile submarine squadron, Submarine Squadron 16, from its operational base at Rota, Spain, northwest of Gibraltar, giving easy access to Atlantic Ocean patrol areas.

Anticipating that this would take place, Chief of Naval Operations James L. Holloway III ordered studies to select a new refit site on the East Coast of the United States.

Four days later, USS James Monroe entered Kings Bay and moored alongside Simon Lake's starboard side to begin a routine refit in preparation for another nuclear weapons deterrence patrol.

On 23 October 1980, after a one-year environmental impact study was completed, and with Congressional approval, the Secretary of the Navy announced that Kings Bay would be the future home port for the new Trident-missile submarines in the Atlantic Ocean.

The decision to base the Trident submarines at Kings Bay started the largest peacetime construction program ever undertaken by the U.S. Navy.

A high-level nuclear weapons policy review recommended that the U.S. Navy reduce its number of Trident Fleet Ballistic Missile submarines from 18 to 14 by 2005.

Specifically included in these responsibilities are the proper integration and coordination of the facilities dedicated to training support of the Trident system.

For protecting submarines the Navy requested a slightly modified design, which added gyrostabilized machine gun, with advanced optics, which was fired under remote control from the ship's bridge.

The Trident Refit Facility (TRF) is the largest tenant command at Kings Bay and has kept a significant portion of the United States Fleet Ballistic Missile submarines at sea since 1985.

TRF provides quality industrial-level and logistics support for the incremental overhaul, modernization, and repair of Trident submarines.

The United Kingdom's Vanguard-class submarines, through the Polaris Sales Agreement, also uses the Trident missile and their sailors sometimes visit the Kings Bay Naval Base.