A device and a method for operating a fuel filter (1) with a diaphragm (16) for cleaning water separated from the fuel, comprising a collecting chamber (9) for the water geodetically arranged at the bottom in a housing (2) of the fuel filter (1), are proposed, comprising at least one sensor (10, 11) each for the maximum (10) and for the minimum (11) water level in the collecting chamber (9), by means of which a valve (13) for discharging the water from the collecting chamber (9) arranged between the collecting chamber (9) and a water purification device (14) containing the diaphragm (16) is controllable. A detection device (21) for detecting the flow behavior of the water between the collecting chamber (9) and the water purification device (14) is present with which at least the time interval (t) of the change of the water level between a signal of the sensor (10) for the maximum and of the sensor (11) for the minimum water level is detectable and in that a computing and memory unit (27) for the evaluation of the signals in the detection device (21) and for signaling (28) a deviation from a predetermined flow behavior of the diaphragm (16) is present.