The increasing use of rare earth elements (REEs) in many industrial sectors and in medecine, causes discharges into the environment and particularly in estuarine areas subjected to strong anthropogenic pressures. Here, we assessed the distribution of REEs along the food web of the Loire estuary. Several species representative of different trophic levels were sampled: 8 vertebrates, 3 crustaceans, 2 mollusks, 3 annelids and 4 algae, as well as Haploops sp. tubes rather related to sediment. The total REE concentrations measured by ICP-MS were the highest in haploops tubes (141.1 ± 4.7 μg/g dw), algae (1.5 to 34.5 μg/g dw), mollusks (9.9 to 12.0 μg/g dw), annelids (0.7 to 19.9 μg/g dw) and crustaceans (1.4 to 6.3 μg/g dw) and the lowest in vetebrates (0.1 to 1.6 μg/g dw). The individual contribution of REEs was, however, similar between most studied species with a higher contribution of light REEs (76.7 ± 7.6 %) compared to heavy REEs (14.1 ± 3.7 %) or medium REEs (9.2 ± 5.8 %). Trophic relations were estimated by stable isotope analysis of C and N and the linear regression of δ15N with total REE concentrations highlighted a trophic dilution with a corresponding TMS of −2.0. The tissue-specific bioaccumulation investigated for vertebrates demonstrated a slightly higher REE accumulation in gonads than in the muscle. Finally, positive Eu, Gd, Tb and Lu anomalies were highlighted in the normalized REE patterns of most studied species (especially in fish and crustaceans) which is consistent with results in the dissolved phase for Eu and Gd. These anomalies could either be due to anthropogenic inputs or to various bioaccumulation/elimination processes according to the specific species physiology. This study, including most of the trophic levels of the Loire estuary food web provides new insights on the bioaccumulation and trophic transfer of REEs in natural ecosystems.