The Corps of Engineers will normally dredge a narrower bit of the channel at a chokepoint and thus the water depth can be maintained if only for one way traffic.
The article I linked to seems to say that dredging won't be possible at places like Thebes, IL since the river bottom is rock along that stretch of the Mississippi. Although if the situation is dire enough, I suppose the Corps can always find a way to deepen the channel there but that would take so long that I doubt that kind of project would alleviate any stoppage this winter.
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