The paper summarizes the results of longterm research on the of influence of some environmental factors (temperature, salinity and anoxia, pollution) on the biochemical status of aquatic organisms that inhabit the lakes of the Republic of Karelia, adjacent areas, and the White Sea. The possibility of applying different biochemical parameters for assessing the status of fish, mollusks, as well as for studying their adaptation strategies and mechanisms depending on the nature of the influencing factor or pollutant is shown. The features of change in the activity of enzymes and isozymes of the energy and carbohydrate metabolism, lysosomal nucleases, cysteine-dependent intracellular lysosomal proteinases (lysosomal cathepsins and calcium-activated cytosol proteinases) in the lipid and fatty-acid composition of membranes in response to environmental impacts are considered.