In a polymetallic ore concentration area, large-scale mining activities can dramatically increase heavy metal concentrations in river sediments, and their temporal–spatial variation and source apportionment are significant for understanding heavy metal migration in rivers and formulating management strategies for environmental protection and the mining industry. Sediment samples were collected along the Yu River, which flows through the Luanchan polymetallic ore concentration area in China, during high-water period (HWP), low-water period (LWP) and flat-water period (FWP) to assess the pollution level and identify the sources of Mo, Cr, W, Cu, Zn, As, Cd, Pb and Hg in the sediments. The findings revealed that Mo, Cd, W, Zn, Pb and Cu were the main pollutants, and Hg was extremely high at some specific locations. Sediments in the upstream region of the Yu River were more severely polluted by heavy metals and had greater ecological risk due to stronger mine exploration. Furthermore, consistent distribution patterns of various heavy metals during different seasons were not found. Some sharp decreases in heavy metal concentrations between adjacent sediments were observed; moreover, at some sites, heavy metal concentrations during LWP and FWP were lower than those during HWP. The results indicated that heavy metals in the Yu River mainly migrated in dissolved form. Mo, Cu, Pb and As for HWP, Mo and As for LWP and Mo, Cr and W for FWP mainly originated from Mo/W mines. Pb/Zn mines contributed to the amounts of W, Zn and Cd during HWP, Cu, Zn, Cd and Pb during LWP and Cu, Zn, Cd and Pb during FWP. Hg was mainly attributed to Au mines, and Cr was the geogenic element. The results could contribute to the sustainability of the mining industry and the formulation of science-based remediation and protection strategies for the rivers near mining areas.