Pathogens present in animal fecal deposits excreted to land undergo a poorly defined process of dispersion, transport or attenuation, and inactivation. The transport of pathogens overland in surface runoff is clearly responsible for event-related increases in the concentrations of in-stream waterborne pathogens in many watersheds. However, there are significant knowledge gaps concerning the precise mechanisms of pathogen transport. This article reviews the fate and transport of pathogens in watersheds supplying drinking water, from their deposition in feces and septic seepages on land to their dispersion in major tributaries. Pathogens considered representative of those associated with waterborne disease included enteric viruses derived from human fecal contamination, bacterial pathogens represented by Escherichia coli O157:H7, and the protozoan pathogens Cryptosporidium and Giardia. References to suitable model and index organisms for these pathogens are described. The key processes determining the fate and transport of pathogens within watersheds are discussed in the context of changing agricultural practices, climate, and scale factors. A generic conceptual model for watershed processes is described in light of the knowledge gaps identified from this review. Future areas for fundamental research were identified and included: (1) inactivation kinetics of pathogens in soil and fecal matrices; (2) characterization of the particle sizes with which pathogens are transported; (3) characterization of pathogen properties and watershed-specific features that affect terrestrial transport and attenuation; and (4) the inactivation and sedimentation of pathogens during their initial introduction to the aquatic environment. Such information is critical to advance the assessment of pathogen total maximum daily loads (TMDL), determining management priorities and appropriate control points, as well as integrating pathogens within the broader watershed hydrologic models.