Appropriate manure application rates, timing, and methods are necessary to maximize nutrient utilization by plants from manure, while minimizing water resource pollution potential, including that of enteric organisms. A field study and a soil column study examined the response of indicator bacterial densities in subsurface drain water to different swine manure applications. The field study focused on the impacts of different manure management regimes on fecal coliform, fecal streptococcus, and Escherichia coli (E. coli) densities in subsurface tile drain water. Eight swine manure treatments were compared with a control treatment where commercial urea ammonium nitrate was applied. Manure treatments included fall injection, spring injection, and late winter broadcast at application rates of 168 kg N/ha and 336 kg N/ha. Results indicated that the highest incidence of significantly elevated bacterial levels occurred where manure had been broadcast in late winter at a rate of 336 kg N/ha.