In the San Francisco Bay Area, is there a place where the road goes under the bay and cars drive through it?

Between Oakland and Alameda are two underwater tunnels known as tubes that you can drive through. That may be what you are thinking of. One was built in 1928 and one was finished in 1963. There is a tunnel between Sausalito and the Marin Headlands and if you take one road to the end, you come out at the ocean, a small portion of the beach but not for swimming.

You may have been on the San Francisco – Oakland Bay Bridge. It has 2 levels. The girders and supports on the side block out a lot of light. It would be easy for a young child to believe they were under water. "10 lanes (5 westbound on upper level, 5 eastbound on lower) of I-80" The Yerba Buena tunnel would add to the effect. "Yerba Buena Tunnel Traveling through the westbound Yerba Buena tunnel Connecting the two halves of the bridge is Yerba Buena Tunnel, measuring 76 feet (23 m) wide, 58 feet (18 m) high, and 540 feet (160 m) long.[10] It is the largest diameter transportation bore tunnel in the world.[3]" Consider Daddy's words as experience enhancement for a young boy.

Well I live in the bay and I don't know if cars can go under tunnels unless ur talking about the bart. Bart is a transportaion that takes u under ground it also might take u under water!