A method of simultaneously cleaning and disinfecting an industrial water system is described and claimed. The method involves the addition to the water of the industrial water system of a Compound selected from the group consisting of the alkali salts of chlorite and chlorate and mixtures thereof; and an acid, followed by allowing the water in the industrial water system to circulate for several hours. The reaction of the alkali salts of chlorite and chlorate and acid produces chlorine dioxide in-situ in the water of the industrial water system. The chlorine dioxide kills microorganisms and the acid acts to remove deposits upon the water-contact surfaces of the equipment. This cleaning and disinfecting method works in a variety of industrial water systems including cooling water systems.