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Soil moisture content and manure application rate may affect the survival and transport of fecal bacteria released from land-applied manure to subsurface drainage water. The impacts of two soil moisture contents and two manure application rates on the transport of tracer bacteria in subsurface drainage water were studied in lysimeters containing well-structured soils. The lysimeters, with initial soil moisture contents of 11 and 19% from 0 to 15-cm depths, received nalidixic acid resistant Escherichia coli (E. coli) strain KS-2 incorporated in the swine manure, and then applied with manure at application rates of 28,000 and 84,000 L/ha. Simulated rainfall was applied at an intensity of 6.3 cm/h for 55 min, 24 h and 14 days after manure spiked with KS-2 was applied. Higher soil moisture contents resulted in significantly greater (a = 0.10) volumes of subsurface drainage water after the first rainfall simulation but not the second. Strain KS-2 was rapidly transported with water to the subsurface drainage depth of 1.3 m at concentrations greater than 4.23 x 10 5 colony forming units (CFU)/100 mL, and then decreased rapidly to less than 1,000 CFU/100 mL at 14 days. After the second rainfall simulation at 14 days, concentrations again increased to greater than 8,000 CFU/100 mL and then decreased rapidly to less than 200 CFU/100 mL at 21 days. The higher manure application rate significantly increased KS-2 concentrations in subsurface drainage. KS-2 and manure nutrient losses showed significant positive correlations; however, correlations were widely variable among treatments, suggesting the factors and processes of transport affect nutrient and bacteria movement differently. Less than 1% of the applied KS-2 was lost in subsurface drainage water and up to 3.4% was detected in the soil at 25 days. Further research should attempt to quantify both vertical and horizontal transport to subsurface drainage systems.