Methods and apparatus for generation of dual biocides are provided. The electrolytic generation of chlorine as a biocide is employed for further generation of additional biocides within a single system or generator, including bromine, iodine, chlorine dioxide, fluorine, or chloramines from their respective salts and/or precursors. A single on-site generating system produces a combination of biocides for applications of use providing cost, safety and efficacy improvements. Methods of using the disinfecting biocides provide a synergistic effect through simultaneous or sequential applications.