It goes through an immersed tube, the Transbay Tube. The tube is made of two tunnels for trains, and a gallery which people can walk through, in case, say, a train derails. The immersed tube was built on land, and submerged after. It opened on September 11, 1972.

The BART (Bay Area Rapid Transit) system does both. Within the cities of San Francisco, Oakland, and Berkeley, the trains run "underground" through traditional bored and cut-and-cover tunnels beneath the streets. However, the most famous segment of the system is the Transbay Tube, which goes "underwater" to connect San Francisco to the East Bay. This 3.6-mile-long (5.8 km) structure is a massive submerged tube that rests on the floor of the San Francisco Bay, reaching depths of up to 135 feet below sea level. It was constructed on land in 57 massive sections, which were then floated into place, sunk, and connected underwater. Opened in 1974, the tube is one of the world's longest immersed tunnels. In 2026, it remains a marvel of seismic engineering; during the 1989 earthquake, the tube suffered zero structural damage and remained operational, proving that being "underwater" in a modern tube can be even safer than being on an elevated bridge during a tremor.

Excellent question! The answer is both, depending on which part of the system you’re on.

BART (Bay Area Rapid Transit) is a hybrid system that uses different methods to cross the geography of the San Francisco Bay Area:

1. Underwater Sections

• Transbay Tube: This is BART’s most famous underwater section. It’s a 3.6-mile long, steel and concrete tube that sits on the bay floor between San Francisco and Oakland. Trains travel through it at a depth of up to 135 feet below the water’s surface. It’s not a tunnel dug through rock, but a prefabricated tube that was sunk into a trench and sealed.
• This is the only true underwater section of BART.

2. Underground Sections (Tunnels)

• Downtown San Francisco: Almost all stations in San Francisco (like Embarcadero, Montgomery St., Powell St., Civic Center) are in deep underground tunnels bored through rock and soil.
• Downtown Oakland & Berkeley: Sections like the approach to the Transbay Tube from Oakland, and the tunnel through the Berkeley Hills, are also in subway tunnels.
• Other Areas: There are shorter underground segments in other cities like Walnut Creek.

3. Above-Ground & Elevated Sections

A large portion of BART’s system is actually above ground: Most of the routes in the East Bay (e.g., through Contra Costa County to Pittsburg/Bay Point, or south toward Fremont) run on elevated tracks or surface-level tracks along freeway medians.

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Quick Summary by Area:

• Crossing the Bay: Underwater (in the submerged Transbay Tube).
• Downtown SF: Deep underground (subway tunnels).