CHEMSEA, Chemical Munitions Search and Assessment, is a flagship project of the Baltic Sea Region Program and is partly financed by the European Union. The main focus of the project is to locate the dumped chemical warfare agents (CWAs) and sample the surrounding environment to assess the possible threat. The project lasts from the fall 2011 until 2014. CHEMSEA is a transnational collaboration including project partners and associated organizations, including governmental agencies and international organizations. Ocean waters are in a constant flux, making the study of effect of CWAs on fish and other marine biota a challenging task. For the evaluation of the risks of dumped CWAs, triphenylarsine (TPA), sulphur mustard (H), Adamsite (DM) and Clark I (DA) are thought to pose the highest realistic risk to marine biota. The exact effects of these chemicals are not known and no information is available for the detoxification rates of CWAs in fish tissues or other marine organism, such as mussels. During CHEMSEA project, cod and mussels were chosen for chemical analysis. Cod was sampled from different sites of Baltic Sea, covering official and suspected dumpsites as well as reference sites in the western and eastern Baltic Sea. Mussels were studied both in situ caging experiments and in vivo exposure experiments. For in situ experiment, cages were deployed at two different depths at two selected hotspot sites and one reference site in the Bornholm dumping area. Based on hydrographical data, the cages were placed at 35 m and 65 m depths at all stations. The poor oxygen conditions prevailing in the main CW dumping area made caging closer to the sea bottom unfeasible. In vivo experiment, mussels were exposed to mixtures of the arsenic-containing CWAs DA, DM and the tear gas α-chloroacetophenone. The main aim was to evaluate biological responses in mussels induced by CWA mixtures at environmentally relevant concentrations. For chemical analysis, cod urine, bile and muscle tissues were chosen in addition to the whole blue mussels from caging experiments and exposure studies. Sulphur mustard hydrolyses quickly into thiodiglycol (TDG) in aqueous environment. TDG was analysed from cod urine and bile and also from whole mussels. TDG could also be in its oxidised form as thiodiglycol sulfoxide so it was reduced to TDG at the beginning of sample preparation. Analyses were performed using combined gas chromatography–tandem mass spectrometry (GC–MS/MS) and the TDG was detected as its heptafluorobutyrylimidazole (HBFI) derivative. DM, DA and TPA were analysed as their oxidation products using liquid chromatography–tandem mass spectrometry (LC–MS/MS) from cod muscle and mussel samples. The sample preparation for these analyses is laborious and contains homogenization, multiple extractions and filtration. TDG was detected from notable amount of fish urine samples as background level and from few samples as higher level. For arsenic-containing compounds, only oxidized TPA was found from one fish muscle sample. Nothing was detected from caged mussels. However, high concentrations of oxidized DM and DA were measured from exposed mussels. Detailed results and conclusions will be discussed.