In this study, we show that natural phototrophic populations can be probed individually for their in situ delta(13)C signature by linking fluorescence-activated cell sorting and isotope-ratio mass spectrometry (IRMS) using in-line pyrolytic, methylation. This novel methodology greatly improved the resolution in discriminating and tracing the differential carbon (C) pathways at the base of the pelagic food web in the cyanobacteria-dominated Lake Loosdrecht (The Netherlands). Our analysis revealed the co-occurrence of phytoplankton taxa differing by 6-10%(0) in delta(13)C. Predominant micro- and mesozooplankton species reflected this difference as the result of preferential grazing and/ or selective digestion. Flow cytometric (FCM) retrieval of phytoplankton delta(13)C signatures, applied in conjunction with C-13-carbonate labeling, also enabled an assessment of in situ population-specific growth rates. Diatoms and green algae exhibited up to ninefold higher growth rates than those for cyanobacterial species. The coexistence-of phytoplankton populations widely differing in delta(13)C, standing stock, and turnover time has important implications for the interpretation of C transfer in pelagic food webs. Our approach disclosed,a disproportional impact on trophic, cascades by numerically minor phototrophs that otherwise would have gone unnoticed. Despite the abundance of cyanobacterial-derived C, the zooplankton largely rely on eukaryotic algae for growth. Rotifers take a central position in passing on this algal C to the cyclopoid copepod populations in the lake. The bosminid-dominated cladoceran opulation uses both the cyanobacterial- and algal-derived C in approximately equal shares.