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Three different aquatic environments (one deep meromictic lake, Lake Lugano, CH; one shallow meromictic lake, Paul Lake, U.S.A.; and one peat-land crossed by a river, Valle ´e des Ponts, CH) were studied. The physicochemical characteristics of hydrous iron oxides identified in these systems were determined by spatially resolved analytical electron microscopy at the level of individual submicrometric particles. High molecular weight natural organic matter, dominantly polysaccharides (lakes) or humics (peat-land), serves as a template for the formation and growth of these particles and governs their final morphology. Depending on the waters, networked microgranules, ill-defined entities, or quasi-spherical globules were identified. These Fe-C-rich particles also contain large proportions of other elements (e.g., P, Ca, Si); they are thus fundamentally different from pure synthetic iron oxides used in the laboratory to infer their transport and sorptive properties. We show that the morphotypes of aquatic iron oxides are influenced by the combined effect of basic environmental parameters, e.g., the ionic strength, the relative concentrations of total iron and organic matter, the nature of the organic matter, and to a lesser extent the pH in the waters.