The US Environmental Protection Agency may impose treatment regulations, such as mandatory filtration-disinfection of all groundwaters to safeguard against the microbial pathogens, Giardia and viruses, that are being linked to increasing numbers of outbreaks of waterborne disease. Some water systems may seek variances from the required treatment regulations, either on the basis of the nature of the system's raw water quality or on the basis of an alternative treatment technique. In order to develop the methodology for the variance analyses, the performance capabilities of filtration, disinfection, and reservoir storage are reviewed. Particular attention is focused on the removal and inactivation efficiencies for the target organisms, Giardia and viruses. The three variance analyses described in this article are based on estimating the percent of removal and inactivation of target organisms in a particular system in comparison with standard treatment methods. Includes 55 references, tables, figures.