Chemical weapons dumped into the sea after World War II possess growing concern for the marine environment; metal shells of different chemical munitions lying on the bottom are severely corroded and dangerous contents pollute the sediments. Chemical warfare agents (CWAs), such as mustard gas and various arsenic-based compounds (e.g., Clark I and Adamsite) and their degradation products have been detected in noticeable concentrations in sediments at the major dumping sites at the Baltic Sea. Blue mussel caging approach was applied to assess environmental impact of thousands of tons of CWAs at the main dumping site at the Bornholm Basin. Due to the patchy occurrence of the CWAs in the sediments mussel caging method was chosen to deploy the organisms exactly at sites where high CWA concentrations were detected in sediments and to one reference site. Biomarkers representing different biological functions including antioxidant defence, biotransformation, neurotoxicity, lysosomal membrane stability, geno- and cytotoxicity, cellular energy allocation and condition index were investigated. Moreover, tissue concentrations of different CWAs and the possible metabolic derivatives of these compounds were analysed in mussels together with “classical” contaminants, such as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and trace metals. Further, mussel cages were equipped with salinity, temperature and oxygen sensors to follow the fluctuations in the environmental parameters during the two and half month caging time. Environmental parameters indicated mixing of the near bottom water in the lower water layer where the cages were deployed (at 60 meters). Significant biomarker responses were observed at the two contaminated sites compared to the reference site indicating CWA induced effect on molecular and cellular level; however the possible anaerobic conditions and lower food availability in deep waters led to decreased bioenergetic status of the caged mussels. Results of the still on-going chemical analysis will be employed together with the biomarker responses and environmental data in the multi-level integrated impact assessment of the area.