Zoonotic pathogens found in land-applied livestock manure may persist in the soil and be transported by runoff into surface waters, contributing to degradation of water quality. Manure management approaches that reduce the risk of water quality impairment need to be identified. The objective of this study was to evaluate the effect of manure application rate on the persistence of manure-borne pathogens in the soil-runoff mixing zone. Swine manure inoculated with Salmonella anatum was land-applied at four different rates and mechanically incorporated. After manure application, 2 cm deep soil samples were collected over time to evaluate the survival of S. anatum, fecal coliform bacteria and coliphages (somatic and male-specific phages). Pathogen numbers increased in soil as a result of manure application. There was a rapid decline in numbers of Salmonella, fecal coliform bacteria, and male-specific coliphages in the runoff mixing zone with persistence between 6 and 10 days. Somatic coliphages were more persistent, with survival up to 143 days, including survival over winter. Somatic coliphages may be a better indicator of the risk of enteric viruses in the environment than the use of traditional bacterial indicators like fecal coliforms. Manure application rate was correlated positively with the persistence of somatic coliphages but did not relate to survival of indicator organisms with short survival times. Controlling manure application rate may be a means to reduce the risk of some pathogens moving with runoff.