Dredging operations in harbours are recurrent to maintain accessibility and navigational depths. One of the main environmental risks of these operations is the remobilization of contaminants trapped in the sediments, rendering them more bioavailable to the biota. However, regulatory policies regarding the contamination risk of dredging chiefly apply to the disposal of dredged materials rather than the direct impact of the procedure itself. In order to assess the ecotoxicological risk of harbour dredging operations in a polluted estuary (the Tagus, W Portugal), the present study compared bioaccumulation and biomarker responses in field-deployed mussels before and after the beginning of operations, complemented by sediment characterization and risk analysis based on standardized sediment quality guidelines. The results revealed a very significant increase in genotoxicity and oxidative stress from the beginning of dredging onwards, which was accompanied by increased bioaccumulation of toxicants, especially polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). Overall, the results indicate the importance of surveying the direct impacts of these procedures on local contamination, especially considering these sediments had been previously classified as "trace contaminated", according to normative guidelines, and therefore safe for disposal. This study shows the importance of obtaining both chemical and biological data in standard monitoring procedures and that the remobilization of contaminants by dredging operations may be grossly underestimated, which calls for caution when assessing the impact of these activities even in low to moderately polluted areas.