Process for treating effluents containing nitrogen in ammonium form, using a sequential biological reactor (1), according to which: a volume of effluents to be treated in one complete cycle is introduced into the biological reactor in one or more successive fractions by volume, each fraction by volume being treated during a subcycle; each subcycle comprises a phase of feeding with a fraction by volume, and at least a first aerated step, during which total or partial oxidation of the ammonium to nitrites takes place by injection of air or of oxygen into the effluent, a settling out and emptying step taking place after the end of the complete cycle; the weight of N—NH4 to be treated is determined from the volume of effluents in the reactor at the end of the feeding phase, and from the difference between the initial N—NH4 concentration in the reactor and a concentration desired at the end of the aerated step, a maximum aeration time TM is dedicated to the aerated step, and an initial air flow rate Qairinit, for the beginning of the aerated step, is determined by taking into account the weight of N—NH4 to be treated and the maximum aeration time TM.