Iron and manganese are the important redox-sensitive elements in the ocean. Previous studies have established a series of paleo-depositional redox proxies based on the form and content of iron in sedimentary rocks (e.g., degree of pyritization, FeHR/FeT, Fe/Al). These proxies were developed and applied on siliciclastic-rich marine sediments. Although marine carbonate rocks are generally considered to preserve the geochemical signals of ancient seawater, neither Fe nor Mn content in marine carbonate rocks (Fecarb, Mncarb) has been independently used as a proxy to quantify environmental cues in paleo-oceans. Both Fe and Mn are insoluble in oxic conditions (Fe2O3, Fe(OH)3, MnO2), while their reduced forms (Fe2+ and Mn2+) are soluble. Therefore, oxic seawater should have low concentrations of dissolved Fe2+ and Mn2+, and accordingly carbonate rocks precipitated from oxic seawater should have low Fecarb and Mncarb, and vice versa. To evaluate whether Fecarb and Mncarb can be used to quantify oxygen fugacity in seawater, we measured Fecarb and Mncarb of Upper Devonian marine carbonate rocks collected from nine sections in South China. Fecarb of intraplatform basin samples was significantly higher than that of shelf samples, while shelf and basin samples had comparable Mncarb. The modeling result indicates that the dramatic difference in Fecarb cannot be explained by variation in oxygen fugacity between the shelf and basin seawater. Instead, both Fecarb and Mncarb appear to be more sensitive to benthic flux from sediment porewater that is enriched in Fe2+ and Mn2+. Porewater Fe2+ and Mn2+ derive from bacterial iron and manganese reduction; flux was controlled by sedimentation rate and the depth of the Fe(Mn) reduction zone in sediments, the latter of which is determined by oxygen fugacity at the water–sediment interface. Thus, high Fecarb of the basin samples might be attributed to low sedimentation rate and/or low oxygen fugacity at the seafloor. However, invariant Mncarb of the shelf and basin samples might be the consequence of complete reduction of Mn in sediments. Our study indicates that marine carbonate rocks may not necessarily record seawater composition, particularly for benthic carbonate rocks. The influence of benthic flux might cause carbonate rocks’ geochemical signals to deviate significantly from seawater values. Our study suggests that interpretation of geochemical data from carbonate rocks, including carbonate carbon isotopes, should consider the process of carbonate formation.