Submarine canyons play an important role in the transfer of contaminated sediments from shelf areas to the deeper ocean. To evaluate the importance of submarine canyons adjacent to the Tagus and Sado estuaries (Portuguese Margin) as sediment pathway major and trace elements, 210Pb radionuclides, organic carbon, calcium carbonate and grain size were analyzed in fifteen short sediment cores from the Cascais and Lisboa–Setúbal submarine canyons and neighbor slopes at the Estremadura Spur and off Sines. Mass accumulation rates (MAR) vary between 0.02 and 0.40 g cm −2 y −1 with the highest values in the upper Cascais and Lisboa canyons. Mercury and Pb enrichment factors exceed 2 and show a continuously increasing trend since 1950 AD in the upper sections of the Cascais Canyon and in the Lisboa–Setúbal Canyon system, implying an anthropogenic source. Mercury and Pb anthropogenic inventories also present highest values in the canyon heads, which is consistent with its proximity to the Tagus and Sado river mouths. To a lesser extent, the Estremadura and Sines slopes and the deeper sections of the canyons also have slightly increasing Hg and Pb enrichment factor trends towards the present-day. For these areas, with a major influence of pelagic sedimentation, we infer atmospheric transport as a complementary source of contaminants. Therefore, our data suggest that although canyons are preferential conduits to transport sediments to the deep sea when compared to the slopes, Hg and Pb derived from human activities have reached both domains with different intensities down to a depth of 2000 mwd.