Late Devonian (ca. 360 Ma), Early Carboniferous (ca. 330 Ma), and Early Triassic (ca. 250 Ma) manganese deposits in the South China Block support an emerging view that some Mn carbonates form through direct synsedimentary (authigenic) precipitation. These Mn carbonates accumulated on distal shelves and are interbedded with lime mudstone and heterozoan carbonates that accumulated in coastal upwelling environments. Lithofacies, Ce anomalies combined with vanadium, uranium, and molybdenum enrichments indicate that the Mn carbonates were primarily precipitated under anoxic conditions. We provide a robust dataset to clarify the precipitation pathway of these Mn carbonates and explore the implications of using them as proxies of regional shallow water and deep-ocean anoxia. In the studied deposits, Mn calcite encases dolomite rhombs (<10 μm) or aggregates, indicating heterogenous nucleation, which is supported by similar lattice parameters of both minerals with a small lattice mismatch (<2.1%). The presence of micro-sized euhedral rhombs and subhedral aggregates of rhombs, the non-stoichiometric compositions, and characteristic organic matter Raman spectroscopy peaks near the D and G bands in the dolomite nuclei suggest an organogenic origin. Authigenic organogenic dolomite precipitation is interpreted to have preconditioned the sediment with nucleation sites for the subsequent precipitation of Mn carbonates in the shallow seafloor. This is consistent with δ13C values (−2.61‰) of Mn carbonate bulk samples that are slightly lower than coeval seawater (0.31‰, from host rocks), suggesting incorporation of 12C during microbial respiration of sedimentary organic matter during the precipitation of organogenic dolomite and hydrothermal sourced inorganic carbon. The absence of Mn in shallow facies suggests terrestrial input of Mn was minimal. Geochemical and sedimentologic evidence suggests that coastal upwelling delivered manganous anoxic deep waters to the shelves. Eu/Eu⁎ ratios (<1.5) and decoupling of Fe and Mn imply long-range transport of hydrothermal Mn, during which hydrothermal fingerprints were muted through mixing with ambient seawater. The transport of hydrothermal Mn to shelves indicates that the regional deep oceans at the time must have been anoxic, as Mn2+ would be easily oxidized and become insoluble under oxygen-rich conditions, preventing its long-distance transport. This precipitation pathway and depositional model implies that Mn carbonates are a largely unrecognized proxy for tracking ancient oceanic redox fluctuations, particularly during times of well-oxygenated global oceans. Hence, these Mn deposits record at least transient regional deep-ocean oxygen depletion in the generally well-oxygenated Late Paleozoic and Early Triassic oceans. The recognition that this periodic anoxia was broadly coeval with the anoxia-related Hangenberg, Serpukhovian, and Permian-Triassic biotic crises suggests a potential relationship between Mn carbonate accumulation and extinction events.