In order to gain preliminary knowledge about the threat to marine ecosystems due to leakage of chemical warfare agents (CWAs) and other pollutants from rusting bombshells on the seabed, a case study was conducted in a dumping area in the southern Adriatic Sea (depth 200–300 m). Following electroacoustic and magnetometric surveys of the CWA dumping area, an integrated ecotoxicological approach was used. This approach was based on analysis of CWA residues and their metabolites, including arsenic, in sediment and organisms, as well as multimarker methodology including the Health Assessment Index, histological lesion analysis and enzyme assays. Two sentinel species were selected, the blackbelly rosefish [Helicolenus dactylopterus (Delaroche, 1809)] and the European conger (Conger conger L., 1758). Sediment analysis revealed the presence of CWA degradation products, including 1-4-thioxane and 1-4-dithiane. Tissues of fish from the CWA dumping site showed higher levels of arsenic than those from the reference site. Neither CWAs nor their metabolites were detected in fish tissues. Arsenic levels recorded in blackbelly rosefish were well above those reported for other fish species from the southern Adriatic, much higher than the FDA limit for food (2.6 mg kg−1) and close to the LD50 calculated for mammals (20 mg kg−1 body weight). The presence of pollutants in the CWA dumping site was also confirmed by pathological lesions in both species and EROD activity, two to three times higher than in fish from the reference site (16.45±8.08 and 8.05±5.87 pmol min−1 mg protein−1 in blackbelly rosefish and 269±24.92 and 78.71 pmol min−1 mg protein−1 in European conger, respectively). Cholinesterase activity seemed unaffected in muscle of both species, whereas in brain they were one-third of those recorded in fish from the reference site (14.22±10.05 and 72.87 nmol min−1 mg protein−1, respectively). This suggests that acetylcholinesterase is sensitive to CWAs. In conclusion, the agreement of all the chemical and biological parameters investigated suggests that the integrated ecotoxicological approach used is appropriate to reveal the presence and biological effects of CWAs in the marine ecosystem.