The Seine is one of the most polluted rivers in Europe with respect to potentially harmful elements. It receives effluents from the upstream Paris urban and industrial area, and also local inputs from the heavily industrialized Rouen and Le Havre regions. The present study deals with this environmental topic and the concentrations of Cd, Ni, Pb, Hg, Zn and Cu were determined in sediment cores collected in the docks basin of Rouen harbour in 2008. The intensity of metal pollution during recent decades was evaluated using an enrichment factor (EF) and a geoaccumulation index (Igeo). The results of vertical distribution showed that the metal pollution in the past is much higher than in the surface sediment. Mercury was found to be the heaviest pollutant (with Igeo and EF exceeding 4 and 20, respectively), and Cd and Pb were the second most important pollutants. A slight contamination in Ni was observed with very low Igeo values. To estimate the sediment toxicity, simultaneously extracted metals/acid volatile sulfides ratio (SEM/AVS) was calculated. Low values of the toxicity index SEM/AVS were observed in the core sediments indicating the inexistence of metal potential toxicity. Also the concentrations of these trace metals were lower than the probable effect concentration values reported as consensus-based sediment quality guidelines for fresh water ecosystems.