A method of detecting water-borne pathogenic bacteria is based partly on established molecular-recognition and fluorescent-labeling concepts, according to which bacteria of a species of interest are labeled with fluorescent reporter molecules and the bacteria can then be detected by fluorescence spectroscopy. The novelty of the present method lies in the use of bacteriophages (viruses that infect bacteria) to deliver the fluorescent reporter molecules to the bacteria of the species of interest. Bacteriophages that selectively infect that species are selected, and fluorescently labeled virus probes (FLVPs) are prepared by staining these bacteriophages with a fluorescent dye. The FLVPs are immobilized on an optical substrate, which could be a window or a waveguide.