Recent advances in gene probe technology have provided the water industry with a powerful new technique for monitoring water supplies for an increasingly complex group of microbes. The basic principles of gene probe technology, including gene probe construction, labeling, hybridization, and detection, are summarized. Recent developments such as chemiluminescent detection systems and nucleic acid amplification are outlined. Environmental applications of gene probe technology to microbes of specific interest to the water industry are discussed and compared with traditional detection techniques. Specific applications include detection of bacteria, viruses, and protozoan parasites. Finally, the potential for application of gene probe technology to the water industry is evaluated. Tables include: 1) summary descriptions of four gene probe systems; 2) advantages and limitations of both gene probe assays and traditional detection methods; 3) environmental applications of gene probe detection of bacteria; and 4) environmental applications of cell culture assays, immunological assays, and gene probe assays for the detection of viruses. Research needs are listed. The article concludes with an extensive reference list. Includes 79 references, tables, figures.