Thieves' Highway - State Belt Railroad
A number of times during the movie we see diesel trains plying back and forth along the Embarcadero. They belonged to the State Belt Railroad system whose purpose was to provide a link between the piers and the four railroad companies serving the city, namely the Southern Pacific, the Atchison, Topeka and the Santa Fe, the Western Pacific and the Northwestern Pacific. The railroad ran between King Street south of Market and the Presidio via a 1500 foot long tunnel under Fort Mason. It began in 1889 using steam locomotives and was finally shut down in 1993 after the loss of most of the port traffic to Oakland. More information can be found here.
Then ... Below is engine number 20, one of a total of six, filmed in front of Shorty's Bar with pier 46 and China Basin in the background.
... and Now, pier 46 has been replaced by a marina and the same viewpoint today looks across South Beach Park towards the AT&T ballpark at China Basin.
Then ... Here we see Nick and Rica walking towards the Colchester Hotel past engine number 23 alongside the Wellman Peck building at the east end of Jackson Street.
... and Now, the corner of the Embarcadero at Jackson has completely changed, as shown below. The Wellman Peck corner building site is now part of this parking lot.
... from 1946 ... Below is an archival photograph of engine number 24 passing below the Bay Bridge.
... and Now, from the same spot we see the train was passing Pier 28, still there today. The railroad tracks have been replaced by the muni tracks of the T Third and N Judah lines.
But wait - take a look at the Bay Bridge in the 1946 photo above. Is that a train passing by on the bridge? It sure is - in the bridge's early years there was an electric train service, part of the privately owned Key System, connecting Oakland and San Francisco. Its two tracks ran along the south side of the lower deck, shared with automobiles using the north side. See the closeup below taken the day the service began, September 23, 1938.