The effects of size, age, and smoltification on muscle protein breakdown systems were studied in wild brown trout Salmo trutta L. inhabiting the Krivoi Ruchey River of the White Sea basin, Kola Peninsula. Activities of autophagy-related proteases including cathepsin B and D, calpains, and proteasome were assayed in the skeletal muscle of brown trout parr and smolt of different age group. Youngest fish group consisted of the most actively growing individuals possessed the higher rate of protein breakdown compared to older groups. Different patterns of muscle protein breakdown inherent to brown trout parr and smolts were shown to be associated with calpain system and cathepsin D activities. Thus, increased activity of these proteases in smoltifying individuals obviously results in amino acid accumulation that could be a mechanism of seawater tolerance required for seaward migration. This study is the first to show the age- and stage-related dynamics in protease activities in skeletal muscle of brown trout inhabiting the Krivoi Ruchey River. Growth- and smoltification-related patterns of protease activities were quite similar in brown trout from the Krivoi Ruchey River and previously studied rivers of the White Sea basin, however, some habitat-related differences were observed.