The method comprises measuring the need for chlorine dioxide treatment, adjusting the quantity of one of the reactants fed to the chlorine dioxide generator to an amount proportional to the measured need for treatment, adjusting the quantity of the second reactant for chlorine dioxide fed to the chlorine dioxide generator to bring the composition of the product stream to a predetermined state. The alkaline earth metal chlorate is selected from the group consisting of sodium chlorate, lithium chlorate, potassium chlorate, rubidium chlorate, cesium chlorate and francium chlorate. The composition of the product stream is determined by monitoring the product stream exiting the generator to determine the composition. The composition of the product stream is determined by monitoring its pH.