The Odiel River runs through an area known as the Iberian pyrite belt in the province of Huelva in the southwestern corner of the Iberian Peninsula. Its waters are acidic and contain large amounts of heavy metals from erosion and mining activity. In addition, the Odiel River estuary is one of the most industrialized areas in southern Spain and, consequently, receives the discharge of industrial and urban waste. Seventeen sediment samples from the Odiel and its main tributaries were analyzed for this study. The chemical partitioning of metals (Cu, Zn, Cd, Pb, Fe, Ni, Cr and Co) in each sample was determined in four fractions (acid-soluble, reducible, oxidizable and residual). The total content of each of the metals was also determined. The results showed high concentrations of Fe, Cu, Zn, Pb and Cd, undoubtedly as a result of contamination from the mining and industrial activity mentioned above. However, the concentrations of the other metals analyzed were low since there are no sources of pollution by them in the Odiel River. Based on the chemical distribution of metals, we found that Cd, Zn and Cu are the most mobile metals (i.e., metals that can pass easily into the water under changing environmental conditions). Cd is the metal that showed the highest percentages in the acid-soluble fraction (the most labile) and the lowest in the residual fraction. However, Pb, Fe, Cr and Ni are present in the greatest percentages in the residual fraction, which implies that these metals are strongly linked to the sediments.