The MCRD San Diego Command Museum is on board the depot (Building 26), and has a collection of artifacts and exhibits for Marines in general and drill and training Marines in particular. The museum is intended to inspire Marines and preserve material and equipment from the drill and combat experience of past Marines since World War II.

There are several Balboa Park museums - The Reuben H. Fleet Science Center, in Balboa Park is a science museum with a planetarium and IMAX theater, suitable for children and with some family material. The San Diego Air & Space Museum, in Balboa Park, has a large collection of airplanes from the dawn of flight through the modern era, including a World War One gallery, World War Two gallery, and jet age gallery. SDASM also offers educational programs, including summer camps. The San Diego Museum of Art has a broad art collection, with a larger collection of Spanish art; SDMA also features educational programs, including the Teen Art Cafe, summer camps, lectures, and other art opportunities. The San Diego Natural History Museum ("the Nat") displays many examples of nature, especially prehistoric animals (usually including something on dinosaurs). The San Diego Museum of Man focuses on people, including many global cultures through history; the Museum of Man also has summer camps and occasional special events.

The Museum of Contemporary Art San Diego specializes in art in all media produced since 1950, and has a education program for kids, teens, adults, and educators.

The San Diego Maritime Museum is a museum of ships, including the USS Dolphin submarine; replicas of ships from the 18th and 16th Century; the Star of India, an actual 19th Century iron sailing bark; and other ships and maritime artifacts. The Museum also draws ships for the Festival of Sail, in late August/early September.

The USS Midway Museum is just down the docks from the Maritime Museum, and consists of the USS Midway herself and several aircraft. The Midway was the longest serving aircraft carrier (1945-1992). Guided and self-guided tours are available.