Denitrification is critical for removal of reactive nitrogen (Nr) from ecosystems. However, measuring realistic, scalable rates and understanding the role of denitrification and other dissimilatory processes in watershed nitrogen (N) budgets remains a significant challenge in biogeochemistry. In this study, we focused on the stream reach and network scale in three Mid-Atlantic coastal plain watersheds. We applied open channel methods to measure biogenic N 2 and N 2 O gas fluxes derived from both in-stream and terrestrial nitrogen processing. A large portion of biogenic N 2 flux through streams (33–100 %, mean = 74 %) was a result of groundwater delivery of biogenic N 2 with the remaining portion due to in- stream N 2 production. In contrast, N 2 O was largely produced in-stream, with groundwater delivery con- tributing on average 12 % of the total biogenic N 2 O flux. We scaled these measurements across one stream network and compared them to hydrologic Nr export and net anthropogenic N inputs (NANI) to a 4.8 km 2 watershed. The N budget revealed that, during the study period, the biogenic N 2 flux through streams was comparable to the difference between NANI and hydrologic Nr export (i.e. the ‘‘missing’’ N). This study provides a methodological and conceptual framework for incorporating terrestrial and in-stream derived biogenic N gas fluxes into watershed N budgets and supports the hypothesis that denitrification is the primary fate of NANI that is not exported in streamflow.