REE + Y concentrations in bioapatite have been repeatedly shown to be ambiguous carriers of information for paleo-seawater reconstructions. The uptake of REE + Y begins rapidly after deposition, and bioapatite can, therefore, potentially record the pore water conditions during early diagenesis. In this study, we examined the REE + Y composition of conodonts belonging to a single species from three coeval facies across the Ordovician Baltic Paleobasin carbonate shelf. We show that the REE + Y concentrations, as well as Ce/Ce*, bell-shape index (BSI), Y/Ho and LaN/SmN ratios, vary systematically in conodonts from facies with different host rock compositions. Dissimilarly, REE + Y patterns and ratios of conodont dental elements from the same facies are uniform, indicating that the local depositional environment imposes principal control on the REE + Y uptake by bioapatite. Furthermore, our results show that even though REE + Y concentrations in different histological tissues of the same conodont vary significantly, no REE-specific fractionation occurs, resulting in similar REE + Y ratios in all tissue types. Our results illustrate that conodonts can record modified seawater-like characteristics of REE compositions if the input of FeMn oxyhydroxides and particulate organic carbon (POC) is low. In contrast, under elevated POC and FeMn oxyhydroxide loading, the conodonts show increasingly positive Ce anomalies and MREE enrichment. Collectively, these results suggest that, although primary seawater signatures are not captured in bioapatite, the conodont REE + Y patterns are controlled by local depositional environments and can record early diagenetic pore water conditions.