A comparative study of the activity of the main lysosomal proteolytic enzymes (cathepsins B and D) in the liver, gonads, muscles, and gills in the White Sea herring, Clupea pallasi maris albi Berg (Clupeidae family), caught in different bays (Onega, Kandalaksha, and Dvina) of the White Sea in autumn was performed. All the studied tissues of herring from the Gulf of Dvina featured an increased level of activity of the lysosomal cysteine protease – cathepsin B, which plays a regulatory role in intracellular protein metabolism. The activity of aspartate protease lysosomes – cathepsin D, the main function of which is the complete degradation of protein molecules, changed only in the gills of herring. The results obtained in the study prove that the lysosomal proteolysis system contributes to the formation of adaptive reactions of fish to specific environmental conditions in the Gulf of Dvina. The Gulf of Dvina, White Sea, is characterized by higher water temperatures, lower salinity and water transparency, siltation of water, lower rates of tidal currents, and increased pollution in comparison to the Gulf of Kandalaksha and Onega Bay. The complex of environmental factors influences lysosomal proteolysis in the tissues of the studied fish, but salinity and the degree of contamination of the bays can be regarded as the key factors.