Flapper Valve Problems. When your toilet fills up after being flushed, the flapper valve allows water to drain into the tank. If the water level falls after the bowl fills up, this valve is probably the culprit.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.