Many toilets really do leak only at night; that’s because people use much less water during these hours and in many municipal water systems, the water pressure rises considerably during this time. It is not uncommon for system water pressure to rise by 15 to 20 pounds per square inch (psi), and by as much as 30 psi in some situations. This rise in pressure could cause “water creep” inside your gravity-fed tank by 1/2 inch or more. That is why the manufacturers of toilets normally suggest that the water level to be set at approximately one inch below the top of the overflow tube.
If you only notice your toilet running in the middle of the night, there is a good chance that the water level in your tank is set too high.