Passenger service ended in 1939, and segments of the structure were partially reused in construction of the San Francisco–Oakland Bay Bridge.

The troubled California & Nevada Railroad had begun construction of a ferry pier in Oakland, but its plans were never realized.

Francis Marion "Borax" Smith purchased the railroad in order to gain access to its right of way and waterfront operations, as well as use the abandoned pier as a starting point for his own passenger mole.

[9] The Oakland, Antioch & Eastern Railway began running interurban cars from Sacramento to the mole starting in September 1913.

[14] In May 1933, an explosion and the ensuing fire destroyed the station building, 500 yards (460 m) of pier, the ferry Peralta, and 14 cars.

After the fire, the California Toll Bridge Authority filed to condemn and acquire part of the causeway as well as the property of the former terminal.

[17] Transbay service was transferred to the bridge on January 15, 1939, though Key System cars and ferries continued to run to serve the Golden Gate International Exposition until the season's closing on October 29.

[19][20] The Bridge Yard building was restored by the California Department of Transportation in the late 2010s and serves as an events space.