@Bombchu Link,
I think there is an entity 191, called 'Water Level' that has the following TSC command:
<ANP0410:0030:0000
Entity 410 is the Water Level entity, which controls the Water Level, which uses the Map background image.
As long as that entity is active, the Water Level will constantly rise and fall around the Y axis of the Water Level entity 191.
Although I do not know exactly how it works, it appears to be the only thing controlling the water level, and after the Core battle, the TSC command listed above is executed, making the water rise to the ceiling. After that, flag 832 is set to make the other Water Level active, also 4000 to bypass the usual death (drowning).
You can use the water level in a mod to actually make the water rise, but usually it is too fast and is impossible to outrun, unless you have unlimited booster, or the Machine Gun.
Another possible way to change the water level is to move the NPC of the water level somewhere else, though I have not yet tested that and it may not work.