To determine nutrient availability and growth rates of phytoplankton on a population level, improvement of discriminative power in fluorescence-activated cell sorting is required. We have combined fluorescence of the endogenous photosynthetic pigments chlorophyll a and phycocyanin with a phosphate deficiency (beta-deficiency) related stain (enzyme-labelled fluorescence, ELF97) that yields green fluorescent precipitates at the site of phosphatase activity, referred to as ELF alcohol (ELFA) fluorescence, to sort phytoplankton from Lake Loosdrecht (The Netherlands). Stable isotope labelling with C-13-enriched CO2 enabled assessment of specific growth rates of sorted populations by pyrolytic methylation-gas chromatography and in-line compound specific isotope-ratio mass spectrometry. The dominant population in the lake, the filamentous cyanobacterium Limnothrix sp., was growing under beta-deficiency in spring, but the availability of phosphate increased in summer. Continuous flow of phosphate-rich medium into a laboratory-scale enclosure of lake water resulted in washout of the cells with ELFA fluorescence, and increased growth rates. In addition, this study revealed population heterogeneity within the cluster of phycocyanin-containing cyanobacteria. ELFA fluorescence thus reflects the level of beta-deficiency of freshwater cyanobacteria and microalgae, but is modulated by metabolic activity of cells within the population.