Over the past 30 years, the significant increasing exploitation of Rare Earth Elements (REEs) for their use in new technologies (e.g. low-carbon energy, multimedia, medicine) has led to their release into the environment. The occurrence of these emerging contaminants in the environment leads to major health and environmental issues. In the last decade, a growing number of studies have observed the presence of anthropogenic REEs in freshwater and marine aquatic organisms. However, limited information is currently available regarding the natural levels of REE concentrations in aquatic organisms. A global understanding of these natural levels is therefore essential to: i) understand the natural biogeochemical cycles of REEs; ii) gain better insights into the risks of exposure associated with anthropogenic REEs; and iii) determine research perspectives by evaluating current knowledge gaps.This dataset compiles concentrations for the 14 stable REEs, from lanthanum (La) to lutetium (Lu), and sum of REE concentrations (∑REE). These data were compiled from 102 articles published over the last 50 years, between April 1973 and January 2023. These articles provided at least one concentration value for one REE in one aquatic organism, regardless of the analyzed tissue (e.g. whole organism, leaf, liver, shell). A total of 15,710 concentration data were compiled for aquatic organisms. The REE concentrations were compiled for in situ aquatic organisms (expressed in µg.kg-1). The available concentration data for water (n=2105; in µg.l-1) and sediment samples (n=1125; in µg.kg-1) from these studies were also compiled. These field data span across a global scale, encompassing both freshwater and marine ecosystems.The REE concentrations were associated with various biological parameters (e.g. Phylum, Species, Habitat, Tissues) and spatial parameters (e.g. Ecosystem, Area). For each of these parameters, the most precise information was obtained from the published articles providing these data. Additionally, the data were classified based on the presence or absence of environmental REE contamination at the sampling site. Further complementary information is available in the dataset (ReadMe tab). The reference for each of the cited articles is also provided in the dataset (References tab).