The Sungun porphyry copper deposit is located 100 km northeast of Tabriz in the Azarbaijan province of Iran. The total concentration and chemical fractionation of metals and metalloids (As, Se, Cd, Cr, Ni, Co, and Zn) in sediment downstream of the Sungun mine was investigated. The degree of contamination was evaluated using the sediment pollution index (SPI) and enrichment factor. The concentrations of As, Cd, Se, and Zn in the contaminated sediments were elevated due to anthropogenic activities. According to the SPI, surface sediments in the ephemeral rivers flowing in the vicinity of the Sungun porphyry copper deposit are classified as natural sediment with no ecological risk, while sediments that received contaminated effluents are classified as slightly polluted. Sequential extraction indicated that Co was principally associated with the iron and manganese oxide fraction, while other elements (As, Zn, Cr, Se, and Ni) were mainly distributed in residual phases. Cadmium is the only element that has a high potential for mobility and bioavailability in the sediments and, of the investigated elements, it poses the greatest potential risk to the local aquatic ecosystems. The chemical fractionation pattern of elements appears to be influenced by industrial effluents. Although the bioavailable fraction of most contaminant metals is low due to the freshness of the sediments, over time, the oxidation of sulfide minerals in these sediments could contribute contaminant elements in soluble form.