The increasing global demand for rare earth elements (REEs) has led to their recognition as emerging contaminants; however, the effect that biota have on the cycling of these elements at the watershed scale is not currently well understood. In this study, water samples and field freshwater clams Corbicula fluminea were concurrently collected along watershed gradients, and concentration profiles of 14 naturally occurring REEs were measured in operationally defined water fractions and soft tissues of the freshwater clams. Moreover, Post Archean Australian Shale (PAAS) normalized REE patterns, fractionation indices, and anomalous values were determined to further extract characteristic features. As a result, both the water and biological samples had variable REE compositions, with higher concentrations of light REEs (LREEs) than middle REEs (MREEs) and heavy REEs (HREEs), while decreasing concentrations were generally observed as filter pore size decreased, implying that large colloidal and particulate fractions were important carriers of REEs. The spatial distribution patterns of REEs revealed a clear site effect among profiles, with variability more pronounced among watersheds and with peaks in sites from a small watershed near the hotspots of the mining area, and then exhibited a decreasing trend with distance from there. Meanwhile, significant bioaccumulation of REEs was observed potentially reflecting different degrees of contamination gradients among the watersheds. The PAAS-normalized distribution patterns tended to be slightly enriched in MREEs, producing a peculiar “roof-shaped” feature and characteristic fractionation. Remarkably, bio-concentration factors (BCFs) highlighted the importance of large colloidal and particulate phases in assessing biologically available REEs for filter-feeding species. Collectively, our study strongly favored that accumulation patterns and fractionation characteristics of REEs in C. fluminea can serve as a reliable indicator of geochemical behavior, providing a promising biomonitoring tool to quantitatively denote different degrees of REE contamination and assess possible impacts in mining watersheds.