Coastal urbanisation exposes surrounding estuarine environments to urban-related contaminants such as polycyclic aromatic hydrocarbons (PAHs), polychlorobiphenyls (PCBs) and pesticide mixtures. Hydrophobic contaminants can adsorb on estuarine sediments. They can subsequently be released on a massive scale in the aquatic environment due to artificial or natural phenomena (e.g. dredging, tides), thereby threatening living organisms. The contamination of sediment is a significant ecological issue in the Seine estuary, France. However, few relevant methods have been developed to assess sediment toxicity and its ecological impacts in a cost-effective way. In this context, we aimed to assess the toxicity of natural sediments from the Seine estuary on the development of the calanoid copepod Eurytemora affinis using a previously developed larval bioassay. This assay involves direct exposure of nauplii to elutriates of sediments for six days. Sediments were collected along the Seine estuary from six polluted sites and one reference site. Pollutants in this estuary included PAHs, PCBs and OCPs (organochlorine pesticides). Nauplius survival was significantly more affected by exposure to all contaminated sediment elutriates, than by exposure to sediment from Yville-sur-Seine (the reference site), whereas nauplius growth was significantly reduced after exposure to contaminated sediment elutriates from four of the six contaminated sites. We identified two distinct site clusters, one including both the sand-rich and the least polluted sediments (Oissel, Quillebeuf-sur-Seine, Caudebec-en-Caux) and the other including both the clay- and silt-rich, and the most polluted sediments (La Bouille, Poses, Pont de Normandie). As expected, survival was significantly more impacted after exposure to elutriates from the second cluster than from the first. This work enables (i) assessment of the toxicity of natural sediments in the Seine estuary and (ii) validation of the larval bioassay previously developed using sorbed sediment with model molecules.