Methods and compositions for cleaning and maintaining chemical, biological and radiological countermeasure washdown systems are disclosed. Systems are effectively cleaned by the removal of water scale, including deposits, sediment, microbiological scale, microinvertebrate fouling, and the like, from the inside surfaces of piping in the system. A section of the system is isolated for cleaning and an aqueous acidic cleaning solution is circulated through the fouled pipe section to be cleaned for a sufficient time and at a controlled pH to dissolve and loosen the scale. After cleaning all of the sections, the system is restored to operational readiness.