In both games, the abyss starts at about 80 metres. Wait, What?
That's the entrance to the abyss. It's implied the "boring" swim down to the abyssal zone is bypassed during the loading sequence between the abyss and its topside entrance hole.
How did the Okeanos sink their temples?
A Wizard Did It. Or maybe A Whale Did It, considering they have a song that drives whales nuts and makes them start smashing things: they just directed them to smash out the supports under the temple (no one said they weren't originally on piers or something).
How do those tanks in the aquarium allow fresh and saltwater fish to live together?
How do the dolphins you befriend in the sequel get to the other places around the world, Gatama Atoll aside? Are they swimming all the way there and following the plane? Or are they plane cargo?