Technical Abstract: Vegetated Treatment Systems (VTS) are a novel method to treat feedlot runoff. Feedlot runoff was collected in a sediment basin, stored briefly and applied to eight treatment areas comprised of perennial grass vegetation. This system is designed to collect excess applied liquid and return it to the sediment basin (recycle system). Traditional fecal indicator metrics in combination with specific assays for manure-borne human pathogens were used to assess the microbiological quality of the VTS runoff, and the survival of bacteria in the soil. Transport of fecal indicators across the treatment areas did not reduce fecal indicator organism concentrations during application. However residual bacterial concentrations in the soil declined over time, and the soil cores taken at the end of the season indicate a 3-5 log reduction of fecal bacteria in the VTS after repeated frequent application. Escherichia coli O157:H7 and Salmonella were cultured from 96% and 85% of runoff samples, respectively, but from less than 1% of the end-of-season soil samples. We conclude that while the VTS does not prevent overland transport of fecal indicators or pathogens at the time of manure application, the system effectively reduces the concentrations of manure-associated bacteria in the soil over time in the treatment areas. This data supports the importance of designing irrigation systems for land application of manures that minimize runoff for limiting pathogen transport. While a VTS was used in this study, the results have implications for any type of land application from feedlots.