Cryptosporidium parvum and Giardia duodenalis are two major protozoa responsible for acute gastroenteritis in North America and Europe. Although water is not the major route of transmission for these protozoa, there have been several documented waterborne outbreaks of Cryptosporidiosis and Giardiasis. The conventional indicators of microbial water quality (coliforms and heterotrophic plate counts) do not necessarily correlate with the presence of Cryptosporidium and Giardia. Moreover, the minimum infective dose of these parasites is very low (30 and 10 for Cryptosporidium and Giardia, respectively). Therefore, the detection of low concentrations of these parasites is necessary. Current analytical methods rely on the concentration of large volumes of water into small pellets and tend to display low recovery rates and a lack of precision. In this study, a flow cytometric and cell sorting approach was used to circumvent some of the drawbacks of conventional analytical techniques. The objectives of the study were to: define the most appropriate flow analysis and cell sorting conditions for environmental samples; evaluate the impact of this analytical approach on the detection of waterborne Cryptosporidium and Giardia; and, apply these conditions to the monitoring of a specific water source.