Total elemental concentrations (Zn, 8–215 ppm; Cu, 3–76 ppm; Pb, 9–66 ppm) vary texturally and regionally in the sediments of the St. Lawrence estuary and open Gulf of St. Lawrence.Chemical and mineralogical analyses indicate that 8–39% of the total Zn, 7–20% of the total Cu and 15–26% of the total Pb are weakly held by fine-grained organic material, oxide grain coatings, ion exchange positions and carbonates in the sediments. These concentrations are potentially available to the biota. The remaining concentrations (61–93% of the total) are not readily available but are locked up in fine-grained sulphide, oxide and silicate minerals.The highest concentrations of the detrital and non-detrital contributions occur in the pelites or muds of the upper estuary. Seaward these concentrations decrease as the natural and anthropogenic supply of dissolved and suspended particulate matter from the St. Lawrence River diminishes. The upper estuary acts as a sink for these elements because most of the non-detrital Zn, Pb and Cu supplied are removed here by adsorption onto fine-grained suspended terrestrial organic material from solution or before entry (Cu) and transferred to the bottom along with other fine-grained material in response to the present depositional conditions. Decreasing concentrations of these elements are deposited seaward and the sedimentation intensities of the non-detrital elements remain constant with fluctuations in total sedimentation intensity in the lower estuary and open Gulf of St. Lawrence.Biogeochemically, Zn is a contaminant and Pb and Cu are potential contaminants of the upper estuary sediments. Zn and Pb are potential contaminants in the lower estuary but all the elements are at or near natural levels in the open gulf sediments.