No single building contains the Maritime Museum of San Diego; rather, its hands-on historians specialize in restoring, maintaining, and operating vessels of historical significance. The fleet is vast and varied, ranging from the Star of India, a 19th-century bark that serves as the museum's oldest active ship, to a B-39 Russian submarine. They are even building an accurate replica of the San Salvador, a Spanish galleon that was the first European vessel to reach the West Coast. The museum uses these vessels to house exhibits, provide tours, and go on excursions into San Diego Bay.

Complementing the ships is the museum's permanent collection of artifacts, which display maritime traditions throughout the ages.