The faecal indicator paradigm as a risk management tool for water undertakers throughout the world has served a useful purpose for well over a century. However, new approaches to risk control and identification are emerging, principally driven by both WHO Guidelines and technological developments in analytical laboratories which offer more rapid microbial enumeration and direct pathogen analysis. Water undertakers and regulators are faced with questions which derive from this rapid development of both regulatory approaches and methodological opportunities. This leads to a series of current science debates in microbiology. Perhaps the most pressing is the relevance of parallel, total coliform and Escherichia coli analyses in the water industry and whether alternative organisms provide better risk assessment and health protection than offered by total coliform analyses. To date, enterococci, sulphite reducing Clostridium spp., Bacteriodes fragilis, Bifidobacteria spp., bacteriophages and non-microbial indicators such as faecal sterols, have been suggested. The extent to which change is justified in the context of emerging Water Safety Plan implementation is explored in this chapter.