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An understanding of the transport and survival of microbial pathogens (pathogens hereafter) in agricultural settings is needed to assess the risk of pathogen contamination to water and food resources, and to develop control strategies and treatment options. However, many knowledge gaps still remain in predicting the fate and transport of pathogens in runoff water, and then through the shallow vadose zone and groundwater. A number of transport pathways, processes, factors, and mathematical models often are needed to describe pathogen fate in agricultural settings. The level of complexity is dramatically enhanced by soil heterogeneity, as well as by temporal variability in temperature, water inputs, and pathogen sources. There is substantial variability in pathogen migration pathways, leading to changes in the dominant processes that control pathogen transport over different spatial and temporal scales. For …