In 1903, when Walker & Co. published this bird's eye view of the area around Fort Point Channel, trains were still king and Boston was full of freight yards, such as the New York, New Haven and Hartford Railroad's yard on the South Boston side of the channel, where it met Boston Harbor. Note how the tracks enter the terminal area, then fan out to different ship berths:
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Also notice how Fort Point Channel continued into South Bay, back when that was an actual bay, and how South Station was way way larger than it is today, stretching all the way to Dorchester Avenue, on land now occupied by the US Postal Service building (and notice how back then the road was actually open to the public):