Human activities directly impact estuaries, where the biota is exposed to sediment contamination. A contamination assessment was carried out in several estuaries in the Southern Iberian Peninsula. Sediment samples were analyzed for the presence of metals/metalloids, and bioaccumulation tests were conducted with clams (Ruditapes philippinarum). Huelva Estuary had the highest contamination levels, while the inner bay of Cádiz and the outer stations of the estuaries from Guadiana, Guadalquivir, Palmones, and Guadarranque were the lesser contaminated. All sampling points (except Huelva) had low contamination levels of As and Cd, but they had high concentrations of Cu. The elements Pb, Cd, Zn, Cu, As, and Hg displayed correlations between the concentrations in sediments and the biota. High bioaccumulation of Zn, Cu, and As was observed in Huelva and Barbate. Important insights into the sediment contamination in Southern Iberian Peninsula estuaries suggest greater management and conservation efforts in these critical ecosystems.