Iron, copper and lead distribution was evaluated in sediment cores from a disturbed mangrove area in Guanabara Bay: a core from a seaward site where mangrove vegetation was removed ~20 yr before sampling (MD); a core from an intermediate site with dead vegetation, apparently due to insect attack (MP), and a core from a landward site with living vegetation (MV). Metal concentrations showed increasing values seaward while organic matter content showed an inverse trend, displaying a negative correlation with metals. This unusual correlation indicates opposite sources, since metals come from the bay and the main OM origin is probably degraded mangrove vegetation. Plant cover loss seems to be a critical factor affecting metal accumulation, particularly due to changes in OM input.