The rare earth elements and yttrium (REY) in bioapatite from deep-sea sediments are potential proxies for reconstructing paleoenvironmental conditions. However, the REY enrichment mechanism and the reliability of this tracer remain elusive because of the lack of key information from ambient pore water. Here, we report high-resolution geochemical data for pore water, bottom water, and bioapatite from deep-sea sites in the western Pacific. Our results reveal that the benthic flux of REY from the deep sea is less substantial than from the shallow marine realm, resulting in REY-rich sediment. The depth distribution of REY in pore water is opposite to that of bioapatite, and REY patterns and neodymium isotopic compositions are not uniformly distributed within bioapatite. These results indicate alteration of REY and neodymium isotopic compositions during early diagenesis. Therefore, we infer that REY from bioapatite are not robust recorders of the deep marine environment through Earth's history.