The Water in the Core's room is used to cool the Core

That's why it is positioned next to the Living Waterway, it is there to control and allow water to move to the core to keep it from over heating. and burning.


Thoughts?

 

Hm, the Core in Cave Story doesn't strike me as something that exactly gets "overheated" and is in need of cooling. Now, the core in Undertale, that's a different story, since it runs on geothermal energy, and relies on those ice cubes from Snowdin town to keep it cool.

While it is curious that the water level in the Core room keeps rising, this doesn't seem to correlate with any sort of change in color that indicates an overheating of the Core. And the Undead Core at the end of the game is able to survive just fine for a prolonged period of time without any water, and things don't get unstable until you destroy it, so I would rule out the idea of that water being used to cool down the Core.

 

I always just assumed the Core room flooded due to the damage from the battle. Causing a rupture in the ancient rock infrastructure keeping the room together, and due to the rooms close proximity to the waterway the water level fluctuates eventually leading to the entire room being flooded by the end of the fight. To prove my point here’s a super accurate and definitely canon map I stole off of amino.

 

I always just assumed the Core room flooded due to the damage from the battle. Causing a rupture in the ancient rock infrastructure keeping the room together, and due to the rooms close proximity to the waterway the water level fluctuates eventually leading to the entire room being flooded by the end of the fight. To prove my point here’s a super accurate and definitely canon map I stole off of amino.

I like your theory better than mine haha