Just to clarify, did you not cap it yet? That would be a definite reason why your water is all messed up.
Hi, sorry that my original post wasn't very clear. I am putting a cap on the red clay, but in my test container I didn't do that. I just finished putting everything into the tank (border of substrate, red clay material inside, then cap). Will be adding water soon-ish so I'll update on how it goes then