A method of measuring a water level in a water trap of a fuel cell system, the method including outputting a detected water level of a capacitive level sensor having a plurality of electrodes in the water trap. The method includes resetting a reference output value of each electrode and determining the water level depending on the speed at which water is introduced while detecting the water level in the water trap depending on an output value measured by the plurality of electrodes. Thereby, the influence of temperature and electrode differences is removed.