Exposure to sub-inhibitory concentrations of antibiotics has been shown to alter the metabolic activity of micro-organisms, but the impact on soil denitrification and N2O production has rarely been reported. In this study, incubation and column transport experiments were conducted on soils exposed to as many as four antibiotics in the ng·kg−1 range (several orders of magnitude below typical exposure rates) to evaluate the impact of ultralow dose exposure on net nitrate losses and soil N2O flux over time. Under anaerobic incubation conditions, three antibiotics produced statistically significant dose response curves in which denitrification was stimulated at some doses and inhibited at others. Sulfamethoxazole in particular had a stimulatory effect at ultralow doses, an effect also evidenced by a near 17% increase in nitrate removal during column transport. Narasin also showed evidence of stimulating denitrification in anaerobic soils within 3 days of exposure, which is concurrent to a statistically significant increase in N2O flux measured over moist soils exposed to similar doses. The observation that even ultralow levels of residual antibiotics may significantly alter the biogeochemical cycle of nitrogen in soil raises a number of concerns pertaining to agriculture, management of nitrogen pollution, and climate change, and warrants additional investigations.