This study represents the first attempt to assess genotoxicity and cytotoxicity effects in herring (Clupea harengus membras), flounder (Platichthys flesus), and cod (Gadus morhua callarias) caught at 47 study stations, located close to chemical munition dumpsites in the Gotland Basin, the Baltic Sea. Herring sampled from stations located in the center of chemical munition dumpsites exhibited the highest levels of micronuclei (MN) and total genotoxicity (ΣGentox), which is defined as the sum of frequencies of such nuclear abnormalities as micronuclei, nuclear buds, nuclear buds on the filament, and bi-nucleated erythrocytes with nucleoplasmic bridges. Exceptionally high and high ΣGentox risks were determined for flounder (89.47%), herring (79.31%), and cod (50%) caught at the stations located close to the chemical munition dumpsites.