An indicator organism is a microorganism whose presence in water suggests the potential presence of pathogenic organisms. Coliform bacteria and E. coli are the most commonly used indicators of water quality.
Indicator organisms are microorganisms used to assess the microbiological quality of water because directly testing for every potential pathogen is impractical and costly. An ideal indicator organism should be present whenever pathogens are present, be detectable by simple and inexpensive laboratory methods, survive in the environment at least as long as the hardiest pathogen, and not reproduce in the environment. Total coliforms, fecal coliforms, E. coli, and enterococci are the primary bacterial indicators used in water quality monitoring. E. coli is considered the best indicator of fecal contamination in freshwater, while enterococci are preferred for marine and brackish water assessments. Bacteriophages (viruses that infect bacteria) and Clostridium perfringens spores are sometimes used as supplementary indicators, particularly for assessing the effectiveness of water treatment processes against viral and protozoan pathogens. The use of indicator organisms forms the foundation of microbial water quality standards worldwide, including the EPA's Total Coliform Rule and the Revised Total Coliform Rule for drinking water systems.