Vascular plants in salt marshes strongly influence processes of heavy metal accumulation. Many studies have focused on this issue; however, there is a lack of information regarding the effects of plants on the distribution of certain poorly studied metals, such as Co, Cr, and Ni. The aim of this study was to comparatively evaluate the capability of Spartina densiflora Brongn. and Spartina maritima (Curtis) Fernald, to accumulate Co, Cr, and Ni and influence the sediment composition around their roots, investigating whether the observed behavior can change with different levels of sediment pollution. Concentrations of Co, Cr, and Ni were determined in tissues of S. densiflora and S. maritima and in sediments and rhizosediments from the Odiel and Tinto marshes (SW Spain), one of the estuaries most polluted by heavy metals in the world. Concentrations of Co, Cr, and Ni in the belowground tissues of both Spartina species were higher than those in aboveground tissues in all sites sampled. Both species showed potential for phytostabilization of Co, possibly by promoting the formation of high amounts of Fe-oxides in the rhizosphere, which can act to retain the metal within the sediment around the roots. In addition, both Spartina species were found to accumulate Co in their roots, thereby avoiding the translocation of this metal to photosynthetic tissues. At the Tinto marsh, there were no differences recorded in metal levels between sediments and rhizosediments of both species, a fact that could be explained by the extremely high background levels of metals at this site, which may impair the ability of the plant to alter the chemistry of the sediment in contact with the roots. The potential for the immobilization of a large amount of Co in the soil, exhibited by S. densiflora and S. maritima, indicates that both species could be highly useful in the phytostabilization of Co contaminated environments.