The morphology and mineralogical and geochemical compositions of the freshwater ferromanganese formations (FMF) of Lake Onego (NW Russia) and small lakes located in its catchment area were studied. The lake waters, bottom sediments and FMF were analyzed by a set of modern methods of geochemistry, mineralogy, and crystal chemistry (powder X-ray diffraction, IR spectroscopy, electron microscopy, ICP–MS analysis, atomic absorption, etc.). A detailed description of the microscopic structure in comparison with the geochemical characteristics of the FMF provides new information on the role of biota in the formation and behavior of individual elements at various stages in the nodule formation process. This study shows the homogeneous composition of microconcretions—only manganese or only ferruginous—in bottom sediments throughout the entire water area of Lake Onego and the rhythmic structures of the nodules, formed by macro- and microlayers with mineralized microbiota. The layers are composed of either crystalline Mn mineral phases (pyrolusite, rhodochrosite) or crystalline Fe mineral phases (siderite, goethite). The separation of Mn and Fe mineral phases in the nodules proceeded during their formation and diagenesis. The examined chemical and mineral compositions, textures, and structures of the nodules are a testament to the hydrogenic source of their ore substance and the formation of FMF is controlled primarily by redox environments at the water–sediment interface.