Few studies have quantified the impact of urbanization on the biogeochemistry of streams at the groundwater-surface water interface, a zone that may be critical for managing nitrogen transformations We investigated the groundwater ecosystem of Minebank Run. a geomorphically degraded urban stream near Baltimore, Maryland in the Chesapeake Bay watershed. Our objectives were to identify the spatial and temporal extent of chemical, microbial, and hydrological factors known to influence denitrification, a microbial process that removes nitrate nitrogen (NO3-) Measurements of denitrification enzyme activity confirmed that subsurface sediments at Minebank Run, especially those with high concentrations of organic carbon, have the capacity to denitrify NO3- Levels of NO3- in groundwater were lower where more dissolved organic carbon (DOC) was available, suggesting that denitrification and removal of NO3 in groundwater were limited by DOC availability Groundwater NO3- was highest when groundwater levels were highest, which, in turn, corresponded to high oxidation-reduction potential (ORP), indicative of high groundwater-surface water exchange Stream flow patterns controlled stream bank and bed infiltration and, subsequently, dictated groundwater levels Declines in water levels likely increased subsurface mixing, which led to low ORP conditions that sustained NO3- removal via denitrification The groundwater-surface water interface is a zone of active nitrogen transformation Management efforts that Increase DOC availability to denitrifiers, reduce stream-flow velocity and flashiness, and increase groundwater residence time will likely improve the nitrogen removal capacity of urban stream channels