The Philadelphia Tunnels won't flood, there a good distance from the Delaware River but the Schuylkill is another story up by 30th Street Station where the tunnels and the River are only a few thousand feet from each other. Course there both above ground but let the river overflow its banks and they will begin to flood quick.
Also don't forget that there is one or two abandoned Stops in the Philly Subway System, one quite large and connecting old Steam Passages throughout some leading quite a distance from Central Philly. I used to ride a bike through them. Tight but doable and completely hidden from most Philadelphians and leading into the sub basements of a lot of older buildings or just dead ending where new construction has obliterated those passage. Don't recommend going down there, easy to get lost and the Bums are scrappers about there territory!
http://hiddencityphila.org/2013/01/t...n-underground/