Stations can't be sealed. How will people enter or exit station, otherwise?Tangent (you started it):
Hyperloop tunnels are sealed to keep the air out (the whole theory of Hyperloop is having trains run in a vacuum to eliminate wind resistance), so presumably if air is kept out than so too shall be water.
The devil's in the details though... Will the stations be underground, or above ground with the tunnels dipping underground from there? If above ground, how far above ground? With climate change in play the historical 100-year flood level ain't what it used to be...