Summary: In many mid-Atlantic watersheds, a large fraction of net anthropogenic nitrogen inputs (NANI) are not accounted for in river discharge. This NANI may be transformed into biogenic nitrogen gases that escape to the atmosphere, or it may be stored in the watershed in groundwater, soil or biomass. The research presented here focuses on developing a streamlined, natural-tracer based method for quantifying biogenic nitrogen gases in streams. We compared different potential natural tracers and calculation methods and explored spatial and temporal variability. Our results supported the use of radon as a tracer of gas exchange in open-channel stream studies, emphasized the importance of biogenic nitrogen gas production in groundwater and not only in bottom sediments, and raised intriguing questions about the behavior of radon and argon, another potential natural tracer, in streams.