Livestock manure applications on fields can be a source of contamination in water resources, including groundwater. Although fecal indicators like Escherichia coli have often been detected in tile drainage systems, few studies have monitored groundwater at depth following manure treatments, especially at sites with a deep, heterogeneous vadose zone. Our hypothesis was that microbial transport through a thick vadose zone would be limited or non-existent due to attenuation processes, and subsurface thickness and heterogeneity. This study tested this hypothesis by monitoring E. coli concentrations beneath a 12-meter thick vadose zone of coarse, heterogeneous glacial sediments, following surface application of liquid swine manure. E. coli were detected on all 23 sample dates over the five month period (04/04/2012- 13/08/2012), with particularly elevated concentrations one week after application and lasting for five weeks. Variable low-level concentrations both before and after the elevated period suggest remobilization and delayed transport of microorganisms to the water table without additional loadings within the flow field. These findings suggest preferential flow pathways allowing deep infiltration of manure bacteria as well as a continued source of bacteria, with variable retention and travel times, over several months. Preferential flow pathways at this site include soil macropores, depression focussed infiltration, and pathways related to subsurface heterogeneity, and/or fracture flow through finer grained diamict beds. Further research is needed to confirm the relative contribution of sources, constrain travel times and define specific transport pathways.