Electron energy-loss spectroscopy (EELS) and elemental imaging under the energy-filtered transmission electron microscope are powerful tools for the characterization of iron-rich particles present in natural waters. Features present in EEL spectra (Fe-M 2,3 Fe-L 2,3 and O-K ionization edges) of goethite (a-FeOOH) have been studied with an energy filter operated at 80 keV to determine optimal quantification and elemental imaging of Fe-rich natural aquatic particles in the 30-200 nm range of thickness. For quantitative aims, the Fe-M 2,3 ionization edge cannot be used easily, but the Fe-L 2,3 edge provides more accurate results owing to a better background extrapolation. The partial cross-section of the Fe(III) M shell has been determined for iron oxide. The use of two-windows (jumpratio) and three-windows (background stripping) imaging methods is discussed in relation to the specimen thickness.