New London was the Navy's first submarine base. In 1868, the state of Connecticut donated 112 acres of land along the Thames River for the Navy's use. Despite being located in the town of Groton, the base became associated with the town of New London when the first Commander of the Navy Yard was called back into service and often stayed at a hotel located in New London.

On October 18, 1915, the USS Ozark brought the first submarines, G-1, G-2, and G-4, to New London. This small force was soon joined by the E-1, D-1, and D-3 brought by the USS Tonopah, and the first ship-turned-submarine, the USS Fulton, was added in 1915.

By the end of World War I, Congress had given over $1 million for the expansion of the base and it grew to include 81 buildings for 1400 men and 20 submarines. From 1930 to 1992, a prominent feature was the Submarine Escape Training Tank, better known as the "Dive Tower," for practice escaping sunken submarines. World War II saw the base grow from its original 112 acres to 497 acres, however after the war was over, many subs were subsequently retired or scrapped.

The first nuclear-powered vessel in the world, the USS Nautilus, called New London home. In 1958 the Nautilus become the first submarine, and ship of any kind, to travel across the Arctic. The Nautilus was retired in 1980, and later became a historic exhibit at the nearby Submarine Force Museum.

New London is home to 15 attack submarines and more than 70 tenant commands including the Submarine Learning Center, Naval Submarine School, the Naval Undersea Medical Institute, and the Naval Submarine Medical Research Laboratory. Almost every submariner in the Navy will be stationed here for training at some point.