Rare earth elements (REE) are increasingly recognized as emerging micropollutants in the environment, and concerns surrounding their presence are steadily growing. However, the understanding of possible pollution and ecological risks of REE in river sediments is relatively scarce. To address this, an investigation into the distribution, origins, pollution levels, and potential ecological risks of REE in sediments along the Jiulong River Estuary and adjacent watersheds was conducted. The results revealed that ΣREE in sediments ranged from 54.98 to 156.05 mg/kg along the Jiulong River and its estuary. The REE concentrations generally decreased from the Jiulong River to the estuary. Cluster analysis and geochemical parameter ratios suggested the high REE concentrations in Jiulong River may be derived from fertilizer and coal combustion. The sediments REE was normalized using the chondrites and exhibited apparent fractionation between LREE and HREE. Additionally, the REE in sediments was characterized by LREE enrichment and negative Ce and Eu anomalies. The evaluation of geo-accumulation and enrichment factors indicated that Gd, Yb, Lu, Tb and Dy were the elements most highly enriched in the sediments. Sites labeled S1–S3 and S5 were classified as moderately polluted, with Lu posing a moderate potential ecological risk, while other elements presented only mild ecological risks. Our findings suggest that anthropogenic activities significantly influence the pollution and potential ecological risks of REE in river sediments. Therefore, attention should be paid to the management of emerging contaminants in rivers and estuaries to protect ecosystems and local populations from potential risks associated with the accumulation of REE in sediments.