Fourier transform infra-red (FTIR) spectroscopy was used to assess carbon allocation in selected phytoplankton (Pediastrum duplex, Ceratium hirundinella, Anabaena flos-aquae) in a eutrophic lake. In contrast to bulk-analysis techniques, FTIR spectroscopy can provide information on carbon allocation at the species level within natural mixed populations. Carbon allocation was determined using lipid/protein (L/P) and carbohydrate/protein (C/P) ratios and multivariate analysis of complete spectra and showed considerable intraspecific heterogeneity within samples dates, and clear seasonal changes in the spectra of Pediastrum and Anabaena, with both alga showing increased L/P and C/P ratios on selected sampling dates. Although increased ratios can indicate nutrient deficiency, the alga were not nutrient deficient during these periods, as indicated by continued population growth and high (>0.1%) internal phosphorus concentrations. FTIR spectra from Ceratium did not show any clear seasonal change. In all three algae, the transition from population growth to decline was not accompanied by any significant change in ratios, nor were low epilimnetic nutrients correlated with increased ratios, marking a significant contrast to laboratory batch cultures (previous studies) where low nutrients and the transition to stationary phase led to marked spectral changes.