I do watch Fringe, and actually think this season (and the whole series) has grown old. But I think your criticism is a bit pedantic for such a very minor point, and besides that the water can plausibly be explained (at least by Fringe standards) by the device allowing the transfer of internal physiology -- so where one suffers internal water damage (or internal bleeding, in the plane crash case), so does the other.

And if that bothers you, I don't know how you can stomach the entire foundation of the show. There are infinite parallel universes based on every different possible choice (a ridiculous concept by itself that somehow allows arbitrary moments of human brain activity to split universes), yet there's only ever contact with just one? And then when Peter reappeared they invented this new "timeline" nonsense to explain how he wasn't from a different entire universe (which I know isn't actually "real" in the series, but it was so stupid that it was embarrassing all the characters bought it for so long)?

Basically, yeah, the water is a bit of a stretch, but if you're going to put up with the show for any length of time, I think you'll just need to accept some sloppy writing and even sloppier physics.