ABSTRACT: Phytoplankton were isolated from natural, heterogeneous populations of particles in Boothbay Harbor, Maine, USA using flow cytometry with cell sorting to measure true rates of nitrogen-specific uptake of ¹⁵N without the bias due to detritus,bacteria or other heterotrophs that affects traditional filtration techniques. After incubation under light or dark conditions with ¹⁵NH₄⁺ or ¹⁵NO₃^-, particles were either directly filteredor were sorted to isolate phytoplankton and then filtered for isotopic analysis. Nitrogen-specific (mu_N, time^-1) and absolute uptake rates (mass volume^-1 time^-1) of ammonium were greater for small (3-10um) phytoplankton than for larger (10-53 um) phytoplankton, whereas the opposite was observed for uptake of nitrate. Accounting for pronounced diel variations in uptake from both nitrogen sources, algal growth rates were calculated to be 0.38d^-1 on ammonium and 0.05 d^-1 on nitrate. The absolute rate of NH₄⁺ uptake by all particles as assayed by filtration was approximately balanced by the summed rates of the 2 sorted fractions and the small (&LT3um) particles that were removed prior to sorting: phytoplankton represented only 50% of the total rate. In contrast, phytoplankton uptake of nitrate represented only about one-third of the total uptake, and the remaining fractions contributed only 10%,leaving about 60% unaccounted for. Future applications of flow cytometry with stable isotopes could be used to investigate diel variations in mu_N and mu_C (carbon-specific uptake rates) and provide an estimate ofphytoplankton growth rates.