Corrected entry: The chambers underneath Barcelona begin flooding when the group activates the mechanism, threatening to drown Nate and Chloe. Two problems here: 1) the chamber that they are in is not watertight, they just closed a flimsy stone door that would leak or burst open and free them; and 2) since these chambers have vents leading to the sewer grates outside (which Sully yells through to communicate), why aren't they already flooded from 4 centuries of rainwater and sewage?
Corrected entry: In the cave, the Baddies were able to steer their boat directly to the ship, while Tom Holland had to dive deep into the water, swim some distance then back up to get to it.
Correction: Before Baddock and co. enter the cave, you hear an explosion, and it is evident in the movie that they blew up the cave's wall to get in with the boat.
You can even see the smoke and debris falling as they pilot the boat through the new hole they just made.
Correction: Water tight does not mean it can't flood. As long as water is going in faster than it is going out, the level will rise. That also explains why it isn't perpetually flooded from rain over the years. If it isn't water tight, it will slowly drain.