Understanding Earth's surface dynamics and biological evolution requires deciphering past marine environmental changes. Hydrogenetic ferromanganese nodules formed by the direct precipitation of Fe–Mn oxide/hydroxide from seawater could record the marine environment at the time of deposition, as in the case of ferromanganese crusts. In this study, petrological and geochemical analyses were conducted on ferromanganese nodules collected from the Japanese Exclusive Economic Zone around Minamitorishima Island in the western North Pacific Ocean. Additionally, the results were compared with those of ferromanganese crusts distributed in the same area to elucidate the secular changes in the depositional environment. The mineralogical features (consisting solely of Fe-vernadite with an absence of 10 Å Mn oxide) and the geochemical characteristics (including positive Ce-anomaly and negative Y-anomaly in rare-earth element patterns, high Co contents, and low Cu and Ni contents) of the nodules suggest that the studied nodules are of a hydrogenetic origin. From the inside to the outside of the nodule, the Mn/Fe and Y/Ho ratios decrease while the Th/U ratio increases, indicating a changing depositional environment over time. A similar trend was observed in ferromanganese crusts from the nearby Takuyo-Daigo Seamount. Furthermore, similar compositional changes were observed on the surfaces of the crust samples (uppermost 1–3 mm), which correlated with depth-related changes in seawater oxygen concentrations. Therefore, the observed cross-sectional changes in the chemical compositions of the nodules and crusts may reflect changes in seawater-dissolved oxygen concentrations over time. The Mn/Fe and Y/Ho trends indicate a shift towards a less oxic environment with increasing age while maintaining the current depth profile, implying an expansion of the oxygen minimum zone (OMZ). Moreover, the observed Ni and Cu enrichment, together with the changes in the Mn/Fe and Y/Ho ratios, suggest that the expansion of the OMZ was caused by increased surface ocean productivity.