There is a specific amount of water that is required to be on the toilet tank. The most likely problem with your toilet is a loose float arm. Only half of float ball should be below water and it will prevent the water from filling too high. Get a plumber to fix the problem.
this is gonna sound gross, but in reality the water in the tank is pretty clean. first you flush so the tank is empty. then you reach in and turn the little nob that controls how much water fills up the tank. thats it.