Measuring water quality is an important application of microbiology. For example, residential or agricultural sewage runoff could contaminate a source of water and make it unsafe to drink. One measure of water quality is the prevalence of coliform bacteria in the water. Coliforms are easy to identify and their presence in high numbers could indicate dangerous levels of fecal or other contamination, which is why they are important indicator organisms.

A relatively easy water quality test uses the Most Probable Number, or MPN, method, and is composed of three phases: the presumptive, confirmed, and completed phases. While the MPN method does not exactly measure the number of coliforms present in a sample, it does give an estimate and can determine whether or not the water is below the safe threshold for potable water.