Eutrophication has been a long-term issue in aquatic environments, where dissolved organic nitrogen (DON) recalcitrance is important. Bioavailable nitrogen qualification and quantification for effluents from stormwater and wastewater are always a challenge. The information in this study deepens the understanding of the interactions between carbon addition and DON decomposition through linear-ditch best management practices for stormwater and groundwater cotreatment. By running a laboratory-scale column study for nitrogen removal using green sorption media, the variation in composition and concentration of DON can be further linked to the population dynamics of microbial species that dominate the nitrification and denitrification processes. With the varying levels of influent total nitrogen concentration, the efficacy of nitrogen removal via biosorption activated media may be realized at the molecular level with ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry.