Rare earth elements (REEs), attractive to society because of their applications in industry, agriculture and medicine, are increasingly released into the environment especially in industrialized estuaries. This study compared the REE distribution in the abiotic compartments: water (dissolved phase (<0.45 μm), suspended particulate matter (SPM)) and sediment of the Loire and Seine estuaries (France). A total of 8 and 6 sites were investigated in the Loire and Seine, respectively, as well as 5 additional offshore sites for the Loire. Total REE concentrations were higher in the Loire for the dissolved phase (93.5 ± 63.3 vs 87.7 ± 16.2 ng/L), SPM (173.9 ± 18.3 vs 114.0 ± 17.8 mg/kg dw) and sediments (198.2 ± 27.9 vs 73.2 ± 27.4 mg/kg dw), explained by higher geogenic inputs. Individual REE contributions along with normalization highlighted heavy REE enrichments and Gd positive anomalies in the dissolved phase of the two estuaries, whereas REE distributions in SPM and sediments followed the natural abundance of the REE classes. The calculated Gd anomalies in the dissolved phase were higher in the Seine (9.7 ± 3.4) than in the Loire (3.0 ± 0.8), corresponding to 88.3 ± 5.1 % and 64.4 ± 11.1 % of anthropogenic Gd. This demonstrates a higher contamination of the Seine estuary, certainly due to the difference in the number of inhabitants between both areas involving different amounts of Gd used in medicine. Offshore sites of the Loire showed lower total REE concentrations (55.8 ± 5.8 ng/L, 26.7 ± 38.2 mg/kg dw and 100.1 ± 11.7 mg/kg dw for the dissolved phase, SPM and sediments, respectively) and lower Gd anomalies (1.2 ± 0.2) corresponding to only 13.3 ± 3.9 % of anthropogenic Gd, confirming a contamination from the watershed. This study comparing two major French estuaries provides new data on the REE distribution in natural aquatic systems.