You can find a brief history of San Francisco-East Bay rail service below. This map shows Transbay rail service at its peak, just after the Bay Bridge opened, when passengers could cross the Bay without transferring to ferries and before the ability to drive across the Bay did to the market for rail what trains on the bridge did to ferries. It may be hard to believe now, but cars were once confined to the upper deck of the Bay Bridge, where there were three lanes each way; below were three lanes for trucks and two pairs of tracks. In the East Bay, the tracks split up as shown below, fanning out into Oakland, Berkeley and surrounding cities and offering much greater coverage, if not reach, than BART does today (several of AC Transit’s Transbay bus routes are direct descendants of Key System lines). On the San Francisco side, connected to the bridge by a viaduct, was the Transbay Terminal, which later became a bus terminal and which has since been replaced by a bigger bus terminal that, one hopes, will someday become a train station. This map obviously takes a modern approach, imagining what a map of the system might look like had it survived.
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