Intracellular partitioning of trace metals is critical to metal detoxification in aquatic organisms. In the present study, we assessed metal (Cd, Cu, Pb, and Zn) handling capacities of mummichogs (Fundulus heteroclitus) in metal-polluted salt marshes in New York, USA by examining metal intracellular partitioning. Despite the lack of differences in the whole body burdens, partitioning patterns of metals in intracellular components (heat-stable proteins, heat-denaturable proteins, organelles, and metal-rich granules) revealed clear differential metal handling capacities among the populations of mummichogs. In general, mummichogs living in metal-polluted sites stored a large amount of metals in detoxifying cellular components, particularly metal-rich granules (MRG). Moreover, only metals associated with MRG were consistently correlated with variations in the whole body burdens. These findings suggest that metal detoxification through intracellular partitioning, particularly the sequestration to MRG, may have important implications for metal tolerance of mummichogs living in chronically metal-polluted habitats.