Rare earth element and yttrium (REY) compositions of bioapatite (e.g., fish tooth and bone) can serve as potential paleoceanographic indicators. However, the REY enrichment of bioapatite and REY transfer from FeMn micronodule to bioapatite remain unclear owing to a lack of comparative study on these processes under variable redox conditions (oxic vs. suboxic), which hampers the utility of these indicators. To address these uncertainties, we conducted in situ geochemical analyses of fish teeth and FeMn micronodules from two REY-rich sediment cores (GC01 and GC02) collected from the Clarion–Clipperton fracture zone in the central equatorial Pacific. We found that the Ce/Ce* ratios of fish teeth from GC01 (sediments ΣREY = 723 ± 274 ppm) and GC02 (sediments ΣREY = 506 ± 65 ppm) gradually increased with depth under oxic conditions, with calculated oxic pore water-derived REY increasing from ∼0–3% on the surface to ∼11–24% at 200 cmbsf. In deep sediment columns (>200 cmbsf), the suboxic pore water contributed a small amount of REY (∼4% to ∼13%) to fish teeth, as evidenced by sharp increases in Ce/Ce* ratios of fish teeth and decreases in Ce/Ce* ratios and increases in Y_N/Ho_N ratios of micronodules. Therefore, the REY-patterns of fish teeth in core-deep samples were overprinted by oxic–suboxic pore waters may be unreliable archives of ancient bottom seawater.