The study area is within the Bor copper mining region, Eastern Serbia, where wastewaters from the Bor metallurgical/smelting facilities have caused serious copper (Cu) and arsenic (As) contamination to the Timok river system. The operating conditions at smelting facilities control the pH of the river waters, resulting in highly acidic waters in 2019 than 2015. This study compares the mobility of Cu and As and risk assessment of river water contamination during both years as well as assessing the risks of riverbed sediments contamination and investigating the origins of Cu and As pollution. In the river system, As generally existed as a particulate species in the entire study area during both years and was widely removed from river waters by sorption onto the hydrous ferric oxides (HFO), whereas dissolved Cu was removed from river waters only at neutral pH conditions with hydrous aluminum oxides (HAO) and HFO at the downstream reservoir site of Timok River. Despite the similarity in Cu mobility during both years, the lower pH of river waters in 2019 than 2015 enabled dissolved Cu species to be transported farther downstream, resulting in a higher level of river water pollution. The contamination factor (CF), used to estimate levels of sediment pollution, had higher values for Cu and As compared to Zn, Pb, Co, and Ni. The CF values of Cu were the highest in sediments near the Bor metallurgical/smelting facilities and at downstream reservoir site, whereas the CF values of As were generally high in the entire research field. Additionally, the ecological risk potential (Er) values of Cu were the highest in sediments of the Bor River and Timok River, reflecting an enrichment of Cu at these sites. Finally, a clarification on the origin of Cu pollution and risks of mobilization was inferred from the sequential extraction test. The predominant Cu species in sediments of the upstream region were oxidizable and residual, hosted by copper sulfides originating from the flotation tailings, suggesting a relatively low risk of Cu release from these sediments. However, at the downstream site (especially reservoir sediments), the contribution of acid‐soluble Cu was 34.8%, suggesting a higher risk of Cu release. The highest contributions of acid‐soluble and reducible Cu (18%) at the reservoir site were promoted by the effective settlement of Cu‐sorbing HAO and HFO. The Cu contents of these two fractions were 0.86 wt%, almost three times higher than that of Cu ore in Veliki Krivelj open pit mine.