The purpose of this study was to estimate one of the important aspects of amphipod laboratory culturing — the effect of different types of nutrition on the key biochemical markers widely used in biomonitoring. The study was performed with the Baikal endemic amphipod species Eulimnogammarus verrucosus (Gerstfeldt, 1858), E. cyaneus (Dybowski, 1874), and Gmelinoides fasciatus (Stebbing, 1899). These species are characterized by different ecological properties and evolutionary history. The results of the study demonstrate that a long-term laboratory exposure to different diets has a direct effect on vital and physiological parameters of the species’ adaptation (mortality, weight, protein concentration). Also, feeding imposes its influence on the common stress-markers of oxidative stress (activities of peroxidase, catalase, glutathione S-transferase), and on anaerobic metabolism (activity of lactate dehydrogenase) in Baikal amphipods, and this effect has a species-specific character. The results should be taken into consideration in future ecophysiological experiments performed with amphipods.