In modern conditions of declining natural sturgeon populations in the Volga-Caspian basin, the role and importance of aquaculture is increasing. In the Astrakhan region, due to the presence of a large natural water fund, cage farming of fish, including sterlet, is widely developed. Cage farming of sturgeon in natural water bodies is associated with the impact of anthropogenic pollution, in this area it is associated with water pollution in the river delta Volga, and the deterioration of the hydrochemical regime, which directly affects fish farming. One of the factors of the negative impact of these changes in the aquatic environment is genotoxicity, the degree of manifestation of which can be assessed using accessible and modern methods, which include micronuclear and DNA comet tests. A serious consequence of the genotoxic effect of pollution is the formation of damage to the DNA of the fish body. The purpose of this work was to assess the frequency of appearance of micronuclei and the degree of DNA damage in the blood cells of juvenile sterlet, as well as the selection of functional additives in food that will reduce the effects of genotoxic pressure from a natural water source. In a scientific laboratory, a series of experiments was carried out on feeding juvenile sterlet delivered from a fish farm in the Volga delta. All juvenile sterlet, both at the beginning and at the end of the experiment, were characterized by a normal physiological state, low levels of DNA comets, and the number of erythrocytes with micronuclei was slightly higher than normal. As a result of experimental feeding, reliable data were obtained that food with the addition of the probiotic drug “Vetosporin-Zh” based on the bacteria Bacillus subtilis contributed to a significant increase in weight gain and body length. All analyzed indicators of DNA comets were significantly lower in the group that was fed with the introduction of a probiotic (the micronucleus test turned out to be less sensitive in this case). The mineral additive “Zeolite” did not show such effectiveness. Thus, the addition of Bacillus subtilis-based preparations when feeding juvenile sturgeon can be reasonably recommended to effectively reduce genotoxic stress for fish, mainly to reduce DNA damage.