Human land use has dramatically increased coastal watershed nitrogen exports contributing to eutrophication. Improved knowledge of sources and transformations of nitrogen in agricultural and urbanizing watersheds will be critical in developing effective coastal catchment restoration strategies. We investigated effects of land use, hydrologic conditions, and aging infrastructure on nitrogen sources and transformations in forest, agricultural, and urbanizing catchments at the Baltimore Ecosystem Study LTER site. We measured changes in N concentrations, annual N exports, σ 15N and σ 18O isotopes of nitrate, and σ 13C and σ 15N of particulate organic nitrogen (PON). Results showed that discharge-weighted annual mean concentrations of N decreased from agriculture to increasingly urban to forest. Seasonal N transformations (nitrification and denitrification) were dominant in all rural watersheds; there were 2:1 linear increases in σ 15N and σ 18O in agricultural and low-residential catchments suggesting the importance of denitrification. In both suburban and urban catchments, stable isotopes indicated that groundwater contamination from sanitary sewers played a disproportionately large role compared to N loading on the land surface from atmospheric deposition and lawn fertilizers. The contribution of wastewater vs. atmospheric derived nitrate increased with storm magnitude suggesting sewage leaks. Restoration of aging sanitary infrastructure did not alter 15N and σ 18O or long-term nitrate concentrations in a stream (but did decrease long-term total N concentrations). Accurate knowledge regarding sources, hydrologic flowpaths, and “hot spots” of denitrification in urban and agricultural landscapes will be critical in minimizing ecological and economic risks associated with catchment restoration strategies and predicting “lag times” in recovery of streams.