Rare Earth Elements and yttrium (REY) in seawater originate from atmospheric fallout, continental weathering, and transport from rivers, as well as hydrothermal activity. Previous studies reported the use of REY measurements in biogenic carbonates as a means to reconstruct these surface processes in ancient times. As coastal seawater REY concentrations partially reflect those of nearby rivers, it may be possible to obtain a regional fingerprint of these concentrations from bivalve shells for provenance and environmental monitoring studies. Here, we present a dataset of 260 measurements of REY abundances by LA-ICP-MS from 42 oyster specimens from six locations in France (Atlantic Ocean and Mediterranean Sea), and from two species (Crassostrea gigas and Ostrea edulis). Our study reports that there is no significant difference in concentrations from shell parts corresponding to winter and summer periods for both species. Moreover, interspecific vital effects are reported from specimens from both species and from the same locality. REY profiles and t-distributed Stochastic Neighbour Embedding processing (t-SNE; a discriminant statistical method) indicate that REY measurements from C. gigas shells can be discriminated from one locality to another, but this is not the case for O. edulis, which presents very similar concentrations in all studied localities. Therefore, provenance studies using bivalve shells based on REY have to be first tested for the species, and are not adapted for O. edulis. Other methods have to be investigated to be able to find the provenance of some species such as O. edulis.