re: What major US city (like top 50) would fare best?

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Didn't think of the Subways... yeah, that could be a major problem.

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Subways have pumps to take care of FRESH water. Salt water, from the ocean, is a different beast. There were multiple tunnels flooded from Sandy that were out for weeks, but that was because of the destroyed electrical equipment from the salt, not the water itself.

Most tunnels have built in pumps to remove rain and groundwater. They might get flooded, but assuming its not salt water, they will return to service after its pumped out.