One of the books, either Historia or Encyclopedia says that the water used to flood Hyrule has magic properties bestowed on it by the gods which don't allow certain races to thrive in it.
I guess it's that way to keep sentient races away from the Hyrule that was flooded so that things like the...
The concept of Zelda's timeline no longer interests me.
But also, as a Nier/Drakengard fan, the Zelda timeline is simple as pie.
True suffering is Taro lore.