The present invention relates to an improved treatment system for inactivating microorganisms. An ion control means generates ions and compensates for conductivity variations in a liquid medium surrounding a microorganism. This increases the microorganism susceptibility to inactivation, by way of an inactivation pulse. A high intensity pulse means used in combination with the ion control means, delivers the inactivation pulse. Exemplary embodiments include a field generator, which generates a field that encompasses the microorganism diminishing ability of the microorganism to regulate proper cellular function, and a pulse pattern switching means. The pulse pattern switching means repeatedly alternates between generating ions by way of the ion control means and delivering the inactivation pulse by way of the high intensity pulse means.