In order to estimate the effects on aquatic organisms of long-term exposure to low doses of yttrium (Y) as a potential emerging contaminant, ecotoxicological and metabolomic data were collected on the model organism Daphnia magna, a keystone species in freshwater ecosystems. Following an initial acute toxicity assessment, a 21-day chronic exposure experiment was conducted using a sublethal concentration of 27 μg L⁻¹ of Y, corresponding to the effective concentrations inducing 10 % effect (EC10) value for mortality endpoint and simulating the environmental Y level in aquatic systems. Results from the 21-day two-factor experiment combining microcrustacean survival, growth and reproduction bioassays and targeted gas chromatography-mass spectrometry (GC–MS) metabolomics indicated significant adverse effects of chronic exposure to Y on D. magna. Daphnids exposed to Y exhibited a significantly lower survival at day 21, delayed the maturity stage, including their first breeding, and decreased clutch size. On the side of metabolomics, a clear and general increase over time of both the number and the level of detected metabolites in the hydroalcoholic extracts of the whole organisms was observed. However, emerging from this broad temporal pattern, several bioactive metabolites were identified (e.g., 2,4-di‑tert‑butylphenol, itaconic acid, 3-hydroxybutyric acid, and trehalose) whose levels in extracts are linked to the presence of Y. These results emphasize the necessity of considering low-dose, long-term exposure scenarios in environmental risk assessments of rare earth elements (REEs), which have often been overlooked in favour of higher concentration studies.