Utile reports  on an interesting proposal by a couple of Yale architecture students: Drain Fort Point Channel south of Summer Street and put the tracks underground there - under a brand-new South Station:
The benefit is a fully subterranean train station, allowing for the redevelopment of both the existing and new track areas for urban development that can knit the Leather District directly to the loft buildings in the Fort Point District.
Just as importantly, the new South Station headhouse will provide views north across Fort Point Channel and Boston Harbor to visitors first arriving in Boston. Only the train station in Venice provides a comparatively dramatic view. Commuters and visitors would find water taxis and ferries directly across Summer Street. Importantly, the new tracks and station could be built while the existing station is fully operational. With only a flip of a switch, trains could be directed into the new station, freeing up the old facility for demolition - except for the historic headhouse, which would be saved as part of a redevelopment plan.
Sounds cool, although, of course, there are some pesky details that would need some attention, beyond the whole idea of building a dam at Summer Street: Gillette uses vast amounts of water from Fort Point Channel at World Shaving Headquarters (although presumably that's why God gave us pipes) and part of the Ted Williams Tunnel goes right under the channel.
Bonus fun fact: There used to be a looped train tunnel under South Station , but it was only used once and later part of it became a bowling alley.
- Downtown 
- The T 
- South Station