A method for treating water containing oxidised nitrogen compounds comprising the steps of: a) providing a microbial electrolysis cell system comprising an anode compartment and a cathode compartment placed on opposite sides of a chamber; a working electrode and a reference electrode located in the cathode compartment; a counter electrode located in the anode compartment; an ion exchange membrane located between the anode and cathode compartments; and a potentiostat, monitored and controlled by a control panel, operatively connected to the working electrode, the reference electrode and the counter electrode, such that it poises the cathode potential in a range from -0.215 to -0.06 V vs Standard Hydrogen Electrode; the system further comprising bacterias able to reduce oxidised nitrogen compounds attached to the working electrode; b) continuously feeding the cathode compartment with an influent of contaminated water with oxidised nitrogen compounds; thereby the nitrogen oxidised compounds are bacterially catalysed reduced to nitrogen gas in the microbial electrolysis cell system by the bacteria attached to the working electrode while the cathode potential is maintained in the range from -0.215 to -0.06 V vs SHE; followed by c) continuosly passing the effluent of the cathode compartment to the anode compartment wherein a oxidation reaction of water to oxygen gas occurs; and d) continuously discharging the treated water as an efluent from the anode compartment, the method further comprising recirculating the water of the cathode and of the anode compartments by respective internal loops (2, 9) placed one in each compartment. a) providing a microbial electrolysis cell system comprising an anode compartment and a cathode compartment placed on opposite sides of a chamber; a working electrode and a reference electrode located in the cathode compartment; a counter electrode located in the anode compartment; an ion exchange membrane located between the anode and cathode compartments; and a potentiostat, monitored and controlled by a control panel, operatively connected to the working electrode, the reference electrode and the counter electrode, such that it poises the cathode potential in a range from -0.215 to -0.06 V vs Standard Hydrogen Electrode; the system further comprising bacterias able to reduce oxidised nitrogen compounds attached to the working electrode; b) continuously feeding the cathode compartment with an influent of contaminated water with oxidised nitrogen compounds; thereby the nitrogen oxidised compounds are bacterially catalysed reduced to nitrogen gas in the microbial electrolysis cell system by the bacteria attached to the working electrode while the cathode potential is maintained in the range from -0.215 to -0.06 V vs SHE; followed by c) continuosly passing the effluent of the cathode compartment to the anode compartment wherein a oxidation reaction of water to oxygen gas occurs; and d) continuously discharging the treated water as an efluent from the anode compartment, the method further comprising recirculating the water of the cathode and of the anode compartments by respective internal loops (2, 9) placed one in each compartment.