The aim of the study was to determine the influence of diets (factor D) and the time period (factor T) during which they were applied on the growth performance and physiological condition (blood plasma hematological and biochemical indicators of stress and immunity) in juvenile sea trout (Salmo trutta; initial body weight approximately 73 g). The diet of the fish that was used prior to the experiment (formulated feed; initial fish sample) was modified as follows: a different formulated feed (group B), mixed feed (feed B + prey fish; group B/N), prey fish exclusively (group N). The fish from group A were given the feed that was used prior to the beginning of the experiment. During the 28-day trial neither factors D nor T influenced absolute or relative fish growth rates. Factor D significantly influenced hematological indicators and leukograms, while the phagocytic index and cidal ability were determined by the time test (factor T). Myeloperoxidase (AMPO) was related significantly with the influence of factors D and T and also with the interaction of D×T. A significant decrease in AMPO was noted after two weeks of the test in groups B, N, and B/N, but after four weeks this indicator did not differ from that confirmed in the initial fish sample. The factors tested influenced stress indicators, i.e., cortisol (D and T) and glucose (D). Significant increases in cortisol (group B) and glucose (groups A, B, and B/N) concentrations were noted after two weeks of the test. After the subsequent two weeks (four weeks of the test) these indicators also stabilized. Sea trout from aquaculture readily accept prey fish; however, changes in diet cause stress reactions such as temporarily reduced immunity. Thus, the procedure for preparing sea trout stocking material for release, which is to change the feed from formulated to natural (live fish), should last approximately four weeks.