A method for filtering the water of an aquarium, a water cultivation tank or similar water bonds, by means of a filtering system comprising a closed vessel and defining a chamber, a filtering body housed in the chamber, a circulation pump having a suction duct, communicating with the aquarium by interposition of a siphon and a delivery duct communicating with the aquarium. Vent means are also provided to eject the air from the chamber. The method comprises the steps of: filling the filtering body with a predetermined amount of water; starting the pump; short-circuiting the pump by means of a fluid passage by putting the delivery duct in communication with the closed vessel; keeping the pump short-circuited at least up to determine the siphon trigger; subsequently stopping the pump; keeping the pump stopped to allow the air to escape from the chamber and the filtering body to be filled with water; re-starting the pump.