Damaged Bowl. A damaged toilet bowl is another problem that causes a water level drop inside your toilet. This is not very common but it does happen. Inspect the bowl and base of the toilet for cracks.f your toilet bowl water level is receding, there is damage to one of the components in the toilet itself. This is a common problem and it is an easy fix as long as you know how to solve it and what to look for. It concerns either the flapper valve inside the tank, the bowl ring or the intake on the toilet.