Microbiological growth on cooling towers, heat exchangers, and piping cause a multitude of issues including microbiologically-influenced corrosion, reduced heat transfer, fill fouling, increased fluid frictional resistance, and dispersion of airborne pathogens such as Legionella. Rapid and effective microbiological monitoring is the key to ensuring that cooling water systems operate safely and efficiently. Flow cytometry has been used for many years in medical applications that involve cell counting and sorting, particularly in cancer research and diagnostics. The ability of flow cytometry to rapidly identify and enumerate large quantities of nano-scale particles and their fluorescent properties creates vast opportunities for applications in bacteria identification and monitoring. This paper examines the use of flow cytometry in conjunction with fluorescent nucleic acid and bacteria strains to rapidly enumerate live and dead bacteria in industrial cooling water samples. Staining methods as a means of identifying particular species, such as Legionella, and cell viability studies using nucleic acid stains are discussed.