There isn't currently a way to seal off blocks or rooms, unfortunately. That does sound interesting, though. I'll have to see how other games handle this and see if I can come up with a way. It probably wouldn't be that difficult to seal them from the top, but I'm not sure how I would handle if you were to open a door or window. That could get tricky.
I will be adding a bit of physics to when you're underwater, and maybe a ship block / buoyancy block in a future update (similar to how the cockpit works for land / air vehicles). But that's all I've really got planned for water stuff so far.