Okay, I guess I'm extremely stupid, because I'm still not able to figure it out with this information. I can move the stone (in its holder) wherever above water level I want, but I don't know where I'm supposed to put it. My first thought is I should get it down to the dark room, but I'm unable to lower the water level to there and I fail to get it out of the floating holder.
I've tried and failed:
* Put it under a ceiling and raise water level. Depending on location, it either sits stuck in the ceiling or suddenly teleports through the ceiling once the water level reaches the upper floor. I can't find any way to manipulate it in the first condition, and the second is basically the same as where it was when I lowered it in the first place.
* Put it on the ledge in the leftmost upper room and lower the water, then wall-jump up to it. Depending on location, either gets stuck on the floor or teleports down to a room I haven't explored yet. Can't see any way to manipulate it still.
* Jump at it in all forms I have (normal, fish, energy, nature, beast).
* Shoot it with energy and a variety of consumed ammunition, as well as sprouts and even the cute bubbles of the fish form.
* Jump over it while pulling.
* Curse at it (don't have a mic though

)
The good thing is, my blundering around has made me find the treasure in the area, which I never would have found if I hadn't tried so hard to find something to get further.