The World Government flooded the world to kill a large part of the population and separated the seas to prevent unification against them.
Why a flood? There are several reasons:
The Noah
This is pretty weak evidence, but Oda seems pretty well versed in Biblical lore (devil fruits, Adam tree, eve tree) and in the Bible, when god decided humanity was too wicked, he flooded the earth and started over with Noah’s family. The presence of an ark in the story suggests to me that at some point a flood happened and it was caused by the gods aka the celestial dragons.
It’s called the great cleansing. This could just be metaphorical, but water is typically used for cleaning. If you’re going to “clean” the world, water is a very literal way of doing that.
Imu Sama
Imu backwards is Umi, the word for ocean in Japanese. Her name suggests he has water powers just like Eneru’s name suggests energy powers. Assuming she is the one who does the cleansing, a flood makes sense. (I also believe that she created the calm belt using her awakening to split the seas further).
The Celestial Dragons decided to move to the top of the redline. Like the Nefertari family, the Celestial dragons all had kingdoms they ruled, but at some point they moved. They had vast land to control by themselves, why all move to the highest point on earth with no resources and shared control?
It seems plausible that the holy land is the one place the flood waters can’t reach. ‘Holy’ because the sea devil can’t reach it. The holy land is kind of a doomsday shelter. (Side theory: the former Alabasta king used the sand-sand fruit’s awaking to save his nation during the flood).
The bubble helmets
When they aren’t in the holy land the celestial dragons are always wearing those silly bubble helmets. They claim that it’s to avoid breathing the same air as everyone, but we know better. They ride slaves and take commoner wives, proximity to commoners isn’t an issue.
Oda has repeatedly shown those bubbles are used primarily for breathing underwater. If there was a giant flood at some point, a group of people paranoid enough to move to the redline might also be paranoid enough to always wear a scuba suit when they leave the holy land.
Theory by EndCentury (https://www.reddit.com/user/EndCentury)
