Given the many developments in water treatment technology over the past century, it may seem surprising that microorganisms have been the cause of more than 75 percent of all waterborne illnesses associated with drinking water in the past 20 years and that outbreaks have more than doubled in the past few years. Are the pathogens also getting more sophisticated? Perhaps not, but new ones do continue to emerge for a variety of reasons. And they present challenges that chemical contaminants do not. For example, they require a human to identify them, and if only a few pass through the water treatment system, they can flourish under the right conditions. In this issue, we look at the major groups of pathogens, how they are detected and treated, and how their abundance varies spatially and temporally in surface waters and groundwaters.