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 N-15 without the bias due to detritus, bacteria or other heterotrophs that affects traditional filtration techniques. After incubation under Light or dark conditions with (NH4+)-N-15 Or (NO3-)-N-15, particles were either directly filtered or 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 (3-10 mu M) phytoplankton than for larger (10-53 mu m) 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 0.38 d(-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 (<3 mu m) 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 of phytoplankton growth rates.