Rare earth element (REE) concentrations in river water reflect both local geological background and the intensity of anthropogenic activities. The increasing demand for high-tech applications is accompanied by an increase in REEs in water environments, especially in urban regions. Therefore, the dissolved REEs in a typical urban river (Yongding River) were analyzed to reveal the influence of anthropogenic inputs. It was found that the sum of dissolved REE (ΣREE) concentrations in river water were 6.27~86.26 ng L−1 (mean 31.05 ng L−1). The spatial distribution of REEs is significantly affected by both natural processes and human activities. To eliminate the effect of upstream land use on downstream measurements, this study established a 500 m buffer zone alongside the river and identified the anthropogenic origin of REEs through correlations among land use proportions within the buffer zone, the population density, and REEs. The Post-Archean Australian Shale (PAAS)-normalized REEs revealed pronouncedly positive Gd anomalies in the range 0.30~20.16 in all river samples. Spearman correlation analysis indicated that the proportion of cultivated land was positively correlated with most of the REEs. A three-dimensional tracer system was established via Gdanth, NO3−/Na+ and Cl−/Na+ to characterize the impact of sewage treatment plants, hospitals and agricultural activities on river water. The results indicate that with the acceleration of urbanization, abnormal REEs can be considered as a sensitive indicator to assess the influence of anthropogenic activities on water ecosystems.