Management of faecal contamination of water would be improved if sources could be accurately identified through water analysis. Human faeces are generally perceived as constituting a greater human health risk than animal faeces, but reliable epidemiological evidence is lacking. United States waterborne disease data suggest that human‐specific enteric viruses account for over half the documented outbreaks. However, in New Zealand, where there is a high grazing animal:human ratio (increasing the relative importance of water‐transmissible zoonoses), it seems prudent to assume that human and animal faecal pollution both constitute a risk to human health. Irrespective of the relative risks, the ability to identify sources would assist in overall management of microbial water quality. Faecal streptococci do not appear to provide reliable faecal source identification. Human and animal sources, respectively, maybe distinguishable by two tests onBifidobacteriumspp.—growth at 45°C in trypticase phytone yeast broth and sorbitol fermentation. Different species ofBacteroidestend to be present in humans and animals, but poor survival in water is a problem. Phages of theBacteroides fragilisstrain HSP40 appear to be human specific, but low counts in effluent in some countries, including New Zealand, may limit their usefulness. Different F‐RNA phage subgroups appear to be associated with human and animal faecal sources. The actinomyceteRhodococcus coprophilushas potential as a grazing animal indicator but it is persistent, and existing culturing techniques are time consuming. The development of DNA‐based techniques, such as polymerase chain reaction (PCR), may assist in the assay of some microbial faecal source indicators. Various faecal sterol isomers offer the possibility of distinguishing between human and animal sources, and even between different animals. Washing powder constituents such as fluorescent whitening agents, sodium tripolyphosphate and linear alkyl benzenes, offer useful human source identifiers. It is unlikely that any single determinand will be useful in all situations, but statistical analysis of appropriate “baskets” of microbial and chemical determinands offers the possibility of identifying and apportioning human and animal faecal inputs to natural waters.