The main objective of this study was to generate measurable input functions to models for predicting the fate and transport of surface water pathogens in watersheds, thereby enabling better management of factors that govern the transport of pathogens to surface waters. A systematic approach was implemented for identifying the industry's research priorities relating to pathogen fate and transport in watersheds. A conceptual model of the relevant processes was developed and the literature describing those processes was critically peer reviewed (Ferguson et al., 2003). Knowledge gaps were identified and considered within the context of the conceptual model. A combination of the magnitude of the knowledge gaps, the benefits of having them narrowed and the resource requirements for doing so provided the basis for setting the research priorities. As a result of this review, the research carried out focused on achieving the following specific objectives: to quantify watershed pathogen sources so as to serve as measurable input functions to models for predicting downstream concentrations; to describe pathogen attenuation as a function of organism characteristics and watershed-specific features (soil type, aggregation and dispersal); to identify and quantify the principal factors affecting pathogen viability in feces and soil, as they transit to local surface water; and, to quantify the influence of the principal factors affecting transport of mobile pathogens passing across the terrestrial environment to local surface water. Pathogen sources and viability, dispersion of Cryptosporidium oocysts, mobility of viruses, and plot studies and rainfall simulation are discussed. Includes 9 references, table, figures.