Morphology and mineralogical and geochemical compositions of freshwater ferromanganese nodules of Ol’khon Island (Sasa Formation) and Kulunda Plain (Lake Porozhnee) were studied. The study has shown rhythmic structures of the nodules, formed by macro- and microlayers with mineralized microflora. The layers are composed of either crystalline Mn mineral phases and finely dispersed Fe phases (Lake Porozhnee) or, on the contrary, crystalline goethite and X-ray amorphous Mn phases (Ol’khon Island). Separation of Mn and Fe mineral phases in the nodules proceeded during their formation and diagenesis. The freshwater nodules show both high (Lake Porozhnee) and low (Ol’khon Island) Mn/Fe ratios. The predominance of Fe phase in the Ol’khon nodules accounts for their high contents of REE, including Ce. The Porozhnee nodules grew, most likely, more rapidly, which is reflected in their low REE contents and Ce anomaly. The examined chemical and mineral compositions, textures, and structures of the nodules testify to the low-temperature hydrothermal source of their ore substance.