The evolution of the impacts of anthropogenic activities in Todos os Santos Bay was evaluated by profiles of trace metals and Pb isotopes determined in sediment cores. Fluxes of metals increased up to 12, 4 and 2 times for Cu, Pb, and Zn, respectively, compared to those recorded in the beginning of the 20th century. Stable Pb isotopes identified a decommissioned lead smelter and burning of fossil fuels as the main sources of Pb. Most metals showed minor to moderate enrichment factors (EF < 4), but Cu and Pb were highly enriched (EF = 28 and 6, respectively) at the Aratu harbor. Temporal changes in sediments were associated to different activities, namely Pb smelting, burning of fossil fuels, maritime traffic, petroleum related activities, inputs of domestic effluents, and changes in land uses. The effects of the implementation of environmental policies to improve the waters of the bay could not be identified in the evaluated cores.