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 did the Singing Dragons maintain a breeding population with such a small number of animals? How did they eat and go up for air if the temple is buried underwater? Also, how would the Okeanos Guardian survive for so long?
The Dragons might just be very long-lived whales, much like the Bowhead Whale.
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?
In Blue World, how do very modern salvageables get deep into places that have been lost and even sealed up for hundreds of years? The Twilight Temple area, I can sort of see, as there's an open area that maybe humans have been discarding things into from above. But the Cavern of the Gods (Zahhab Temple)? Even Valka Castle should have all its modern stuff in a pile at the Well Bottom... and not all the way into the King's Chamber. Or really, anywhere past Spiral Tower.
At least in the case of Valka Castle, it might have been the resident false killer whale picking up and playing with the objects.
How did Valka Castle end up being a mythical place that no one has ever found, when it has a tower sticking right out of the water?