Pathogen transport to surface and groundwater is a serious environmental concern when untreated livestock manure is applied to farmland. Artificially drained farmland is particularly at risk because preferential flow pathways can transport contaminants directly to subsurface drains with no opportunity for filtration. A column study was performed to evaluate the effects of the growth and decay of roots on the saturated hydraulic conductivity (Ksat), miscible displacement of a bromide tracer, transport of E. coli, and breakthrough of the P22 bacteriophage in loamy sand soil. Compared to bare soil, the initial corn growth decreased the saturated hydraulic conductivity (Ksat) at a rate of -0.5 to -0.75 cm/h-week, but Ksat values increased when the corn plants were killed and the roots decayed. Root regrowth caused a slight decrease in the Ksat (0.06 cm/h-week). There was no detectable difference in the displacement of a bromide tracer through the columns due to root growth/decay. When swine manure was applied there was no significant difference between the initial concentration of E. coli in the effluent from bare columns with and without manure. Growing or decaying roots increased the rate of bacterial transport through the soil columns. The recovery of the P22 bacteriophage applied in manure was greater than when applied in deionized water due to a lack of competition for adsorption sites. When applied in manure to a cereal rye cover crop, the bacteriophage broke through and peaked at the same time or slightly before the E. coli . The P22 bacteriophage appeared to be a suitable microbial marker for field testing for linking a manure application with water contamination at the field scale.