I had this same problem, and after reading this thread decided not to worry about it. However, the water did not get clearer no matter how many times I changed the water. It got darker, made a brown film over everything in the terrarium, and the result was a fungal infection that killed one frog and left the other very sick - she is still recovering in quarantine.

I redid the entire terrarium, purchased an external filtration system with a carbon filter and used a thicker layer of hydroballs, and did not put any dirt or wood beneath the falling water, but again the water is brown and only growing darker. My survivor loves to bury herself in the coconut fiber, but I am opting to do away with it alltogether and put a tall foam barrier between the water area and the substrate area, with only rocks in the water area and large wood chips in the drier area.

The instructions they give you on the Hydroballs package are not to be trusted! The natural waterfall is becoming a nightmare.