At present time, due to the deterioration of environment, the pollution of rivers by industrial and domestic wastewater, as well as unsustainable fishing resulted in decrease of Atlantic salmon reserves all over the world. In the north-west part of Russia, the one of few rivers where the natural reproduction of this the most valuable commercial species is preserved, is Varzuga River (Murmansk region). To develop strategies for sustainable conservation of salmon populations the monitoring should be conducted in order to maintain stable living conditions in the river ecosystem. It is known that the enzymes involved in the protein, energy and carbohydrate metabolism are quite informative indicators of fish growth, development and adaptation to environmental changes. Along with parameters mentioned above, lysosomal hydrolyses, including acid nucleases involved in compensatory reconstructions of nucleic acid and the closely related protein metabolism are used to assess the status of aquatic ecosystems. The activity of lysosomal nucleases (RNAse, DNAse) in muscles of different age groups (0+, 1+, 2+) of juvenile Atlantic salmon Salmo salar L. from Varzuga River (Sobachiy porog) was investigated in the present study. It was shown that the activity of enzymes studied and the protein content in skeletal muscles increased linearly and were maximal in two-years-old salmon. The absolute values of lysosomal RNAse activity were slightly higher than DNAse activity. The data obtained indicate that the active participation of lysosomal nucleases in adaptive reactions of juvenile salmon on the early stages of post-embryonic development. First of all, it results in the intensification of biosynthetic processes of protein. To conclude the living conditions in Varzuga River are favorable for the growth and development of juvenile Atlantic salmon.