The results of this paper report the analysis of the fate and transport of wastewater and anthropogenic nitrogen along the Potomac River estuary, from Washington D.C. to the Chesapeake Bay. In conjunction with a mass balance approach, nitrate isotopes were used to estimate fluxes and trace the sources and transformations of N along the estuary. This study shows that estuaries have a large capacity to transform N inputs, but with large seasonal variability due to hydrological extremes.