River water and sediments collected from the Erdenet, Gavil, and Khangal Rivers, near the Erdenet Cu–Mo mine were analyzed for their rare earth elements (REE) and yttrium (YREE) contents. Surface water samples were also collected from the tailing pond and ash pond of the mine, as well as in the seepage from the ash pond, where a part of the effluent flows into the Khangal river. The major chemical compositions of river and surface waters were found to vary slightly with water flow. The river water is Ca–HCO3-dominated in the upstream of the Erdenet and Gavil Rivers and ash pond; Ca–SO4-dominated in the tailing pond and seepage from the ash pond; and Ca–HCO3–SO4-dominated downstream of the Erdenet and Khangal Rivers. Both river and surface water exhibited a significant diatom content and the dissolved organic matter mainly comprise of fulvic acid-like materials, protein-like materials and microbial materials. The concentrations of YREE in river and surface waters ranged from 4.6 to 14.9 ng/L, whereas those of the sediments and rocks were 10–43 mg/kg and 25–34 mg/kg, respectively. Shale-normalized YREE patterns of river and surface waters, irrespective of water type, were characterized by enrichments in the middle REE (MREE) and heavy REE (HREE) relative to the light REE (LREE), exceptionally positive La anomalies, and super-chondritic Y/Ho ratios. The predominant REE species were REE(CO3)2−, REECO3+, and REESO4+ in the Ca–SO4-rich water. The HREE enrichment in both river and surface waters resulted in stronger complexation with carbonate ions and fulvic-acid like materials with increasing atomic number and preferential sorption of LREE onto sediments in neutral to slightly alkaline pH water. The YREE patterns of sediments showed MREE enrichment. Total YREE contents in the river sediments were correlated with Fe2O3, P2O5 and loss on ignition (LOI), suggesting the MREE enrichment fractionated by precipitation of authigenic MREE-enriched minerals such as phosphate, Fe (oxy)hydroxides and organic matter. With the exception of La, there were significant correlations among neighboring YREE concentrations, indicating that most YREEs were fractionated by the same geochemical processes, such as aqueous complexation and sorption onto the sediment surfaces. The concentrations of La did not correlate with those of the other YREE, suggesting that the La anomaly was probably induced by a biogenic activity such as diatom blooming and/or anthropogenic processes. Our results provide better understanding of REE behavior because of (bio)geochemical and anthropogenic contamination in terrestrial water systems.