The Black Sea coastal waters near Sevastopol are used intensively for household and industrial purposes and are characterized by high human disturbance. To investigate the level of environmental toxic impact on the organism functional state, this study analyzes changes in hemolymph cell composition, morphology, DNA content, and cell cycle parameters of bivalve mollusk Mytilus galloprovincialis from six experimental sites. The mollusks from the mussel farm on Donuzlav Lake (Crimea) are the control group. Significant differences have been found between mussels from the control area and coastal waters near Sevastopol in main morphological and functional parameters such as cell size, granularity, and nucleus-cytoplasmic ratio. Mussels from the Sevastopol area are characterized by abnormalities of the hemocyte cell cycle manifested in aneuploidy and an increase in the intraindividual variability of genome size and proportion of cells with 4c DNA content up to 34.80–65.5%, which most likely reflects the cell transition to polyploidy.