Mare Island, near the city of Vallejo, California, was first Naval Base in California. The Napa River forms its eastern side as it enters the Carquinez Strait juncture with the east side of San Pablo Bay. In 1850, Commodore John Drake Sloat, in charge of a commission to find a California naval base, recommended the island across the Napa River from the settlement of Vallejo; it being "free from ocean gales and from floods and freshets."

On 6 November 1850, two months after California was admitted to statehood, President Millard Fillmore reserved Mare Island for government use. The U.S. Navy Department acted favorably on Commodore Sloat's recommendations and Mare Island was purchased in July 1852, for the sum of $83,410 for the use as a naval shipyard. Two years later, on 16 September 1854, Mare Island became the first permanent U.S. naval installation on the west coast, with Commodore David G. Farragut, as Mare Island's first base commander. For more than a century, Mare Island served as the United States Navy's Mare Island Naval Shipyard.

Before World War II, Mare Island had been in a continual state of upbuilding. Then came Pearl Harbor. In 1941, the drafting department had expanded to three buildings accommodating over 400 Naval architects, engineers and draftsmen. Mare Island became one of the U.S. Navy's ship building sites in World War II specializing in building diesel engine powered submarines—they eventually built 32 of them. After the war was over Mare Island became a premier site for building nuclear-powered submarines—building 27 of them.

Naval Base San Diego was started on land acquired in 1920. San Diego has become the home port of the largest naval fleet in the world, and includes two supercarriers, as well as U.S. Marine Corps stations, U.S. Navy ports, and U.S. Coast Guard installations. Naval Base San Diego is the largest base of the United States Navy on the west coast of the United States, in San Diego, California. Naval Base San Diego is the principal homeport of the Pacific Fleet, consisting of 54 ships and over 120 tenant commands. The base is composed of 13 piers stretched over 977 acres (3.95 km2) of land and 326 acres (1.32 km2) of water. The total on base population is 20,000 military personnel and 6,000 civilians.