Two groups of bacteriophages that infect Escherichia coli, somatic and F-specific coliphages, have been used in academia as both fecal and viral indicators for many years. Regulatory authorities in different parts of the world are beginning to consider coliphages as indicators of water quality in a range of settings. However, issues such as their potential replication in natural water environments, the cumbersome detection and enumeration methods, a lack of definition concerning which of the two groups should be included in future regulations, and the lack of a clear correlation between coliphages and human viruses and health risks in different water settings remain controversial. This review attempts to shed some light on these contentious issues. The conclusions are that: 1) supposing that they can replicate in some natural water settings, the contribution of coliphages replicated outside the gut will not affect the numbers contributed by fecal pollution and detected by strains recommended for standardized methods; 2) there are easy, fast, and cost-effective methods that can be used in routine laboratories after a little training; 3) perhaps the best option is to determine both groups in a single step; and 4) the low correlation of coliphages with human viruses and health risks is no worse than the correlation between different human viruses.