The elemental composition of cells of Anabaena flos-aquae was investigated by energy-dispersive electron probe X-ray microanalysis (10 kV) of mixed phytoplankton samples obtained from different depths within a stratified eutrophic freshwater lake. Preliminary studies had indicated that at 10 kV, X-ray information was derived mainly from the peripheral region (up to 1–2 μm) of cells. Routinely detectable elements (present in at least 50% of cells) included Mg (overall mean 112 mmol kg−1 dry mass), Si (1850), P(313), S (113), Cl (92), K (300) and Ca (56). Peaks of Na and Al were also frequently present. Individual elements showed a wide range of intracellular concentrations at each depth within the lake. Si had a clear bimodal distribution at depths of 1–8 m, indicating both low-Si (mean concentrations 54–290 mmol Si kg−1) and high-Si (2770–3800 mmol Si kg−1) cell subpopulations. Low-Si cells had significantly higher concentrations of other detectable elements compared with high-Si cells, but could not be distinguished from the latter in terms of morphology or stage of cell cycle (comparison of dividing and non-dividing cells). High-Si cells were intermixed with low-Si cells in individual Anabaena colonies and decreased proportionally with depth, ranging from approximately 75% in the surface sample to 10% at 8 m. With the exception of Si, mean elemental concentrations of Anabaena populations were closely similar throughout the epilimnion. These differed from the metalimnion sample, which had significantly higher concentrations of Mg, P, S and K, and a lower concentration of Si. Mean ratios of certain elements (Mg, P, S and K) and ion groups (monovalent/divalent cations) were highly constant throughout the sampled water column. At each depth, most of the cell elements were significantly and positively inter-correlated (Pearson analysis), with Mg, P, S and K typically constituting the major group (factor analysis). Correlations with Si were invariably negative, suggesting a separate (possibly cell wall) location of this element in the cell.