Woodchip denitrification bioreactors are an important edge-of-field practice for treating agricultural drainage; however, their ability to filter microbial pollutants has primarily been explored in the context of wastewater treatment. Upflow column reactors were constructed and tested for E. coli, Salmonella, NO3-N, and dissolved reactive phosphorus (DRP) at hydraulic retention times (HRTs) of 12 and 24 h and at controlled temperatures of 10 and 21.5 °C. Influent solution was spiked to 30 mg L−1 NO3-N, 2–8 × 105 E. coli and Salmonella, and 0.1 mg L−1 DRP. Microbial removal was consistently observed with removal ranging from 75 to 78% reduction at 10 °C and 90–96% at 21.5 °C. The concentration reduction ranged from 2.75 to 9.03 × 104 for both organisms. HRT had less impact on microbial removal than temperature and thus further investigation of removal under lower HRTs is warranted. Nitrate concentrations averaged 96% reduction (with load removal of 14.6 g N m−3 d−1) from 21.5 °C columns at 24 HRT and 29% reduction (with load removal of 8.8 g N m−3 d−1) from 10 °C columns at 12 HRT. DRP removal was likely temporary due to microbial uptake. While potential for removal of E. coli and Salmonella by woodchip bioreactors is demonstrated, system design will need to be considered. High concentrations of these microbial contaminants are likely to occur during peak flows, when bypass flow may be occurring. The results of this study show that woodchip bioreactors operated for nitrate removal have a secondary benefit through the removal of enteric bacteria.