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Vegetated fulter strips (VFS), as a best management practice, have become an important component of the water quality improvement in watersheds. The SWAT model allows for a comprehensive description of agricultural practices, and has proven to be efficient in applications to watershed with a substantial agricultural component. The REMM, KINEROS, and other models have recently been suggested to use SWAT output to evaluate the VFS retention capacity with respect to nutrient and sediment loads. The concern about the manure-borne pathogens in waterways and water bodies has to be addressed in more details by estimating the efficiency of VFS in pathogen retention. The existing knowledge base shows that the functioning of VSF as barriers for manure-borne pathogens to the large extent depends on vegetation status, soil infiltration capacity in VFS, and rainfall intensity and duration. The effect of these factors on the pathogen breakthrough in VFS needs to be researched at the time scales smaller than the computation interval of one day that SWAT uses. The downscaling of the SWAT output to the smaller time scales, however, introduces an uncertainty. We have developed the model STIR to simulate the overland transport and loss to infiltration of manure-borne pathogens in VFS. This model was used in Monte Carlo simulations to evaluate the possible variability in pathogen breakthrough in VFS with inputs from SWAT. The simulations show that probabilistic characterization of the VFS efficiency with site-specific soil and weather properties can be useful in making decisions on VFS placement with respect to manure-borne pathogens.