Abstract. Anthropogenic alteration of the form and concentration of nitrogen (N) in aquatic ecosystems is widespread. Understanding availability and uptake of different N sources at the base of aquatic food webs is critical to establishment of effective nutrient management programs. Stable isotopes of N ( 14 N, 15 N) are often used to trace the sources of N fueling aquatic primary production, but effective use of this approach requires obtaining a reliable isotopic ratio for phytoplankton.In this study, we tested the use of flow cytometry to isolate phytoplankton from bulk particulate organic matter (POM) in a portion of the Sacramento River, California, during riverscale nutrient manipulation experiments that involved halting wastewater discharges high in ammonium (NH + 4 ). Field samples were collected using a Lagrangian approach, allowing us to measure changes in phytoplankton N source in the presence and absence of wastewater-derived NH