If you hear your toilet fill with water every couple of minutes, but no one has used the toilet you may need a new flush kit. This is a simple fix. We will replace the flush kit and flapper in the tank of the toilet. The toilet runs every couple of minutes because: instead of flushing the toilet and all the water draining out of the tank, the flush kit is allowing water to slowly leak out. The toilet flush kit will kick on when the water level is too low (thinking that the toilet has been flushed) and fill the tank up with water to the proper level. This is why you hear the toilet every couple of minutes.