Feed additives containing probiotic microorganisms can have a beneficial effect on fish productivity, contributing to the formation of a natural intestinal microbiome. At the same time, the aquaculture industry is actively developing innovative methods and technologies, reducing adverse environmental impacts. The novelty of the work is confirmed by trends in the search for the development of environmentally friendly approaches using species-specific bacteria to increase fish productivity in the industrial aquaculture system. The purpose of the studies was to study the antagonistic activity of species-specific bacteria in laboratory conditions when they are cultivated in different temperature modes and their use as a feed additive to increase the productivity of Russian-Lena sturgeon. Species-specific bacteria Pediococcus acidilactici CEEM B-063 and Enterococcus faecium CEEM B-064 isolated from the gastrointestinal tract of crucian carp (Carassius) were used and used to obtain a candidate feed additive. Pathogenic aeromonad species—Aeromonas salmonicida 120,056, Aeromonas jandei 120,054, Aeromonas hydrophyla 120,060 were used as indicators to study the activity of probiotic properties of species-specific bacteria. Using biotechnological methods and approaches, a feed additive was obtained by accumulating a bacterial mass in a bioreactor and its subsequent freeze-drying. A high probiotic potential of species-specific microorganisms was established at different cultivation temperature modes. The temperature of 14–16 °C was optimal for growth, at which the bacteria maintained their viability and antibacterial activity. The candidate probiotic microorganisms Pediococcus acidilactici CEEM B-063 and Enterococcus faecium CEEM B-064 were added to lyophilized fish feed in an amount of 1–2% and the viable cell concentration of each microorganism was 1 × 109 CFU/g. When studying the effect of the developed probiotic additive on the productivity of Russian-Lena sturgeon, an increase in the average daily and absolute growth of live weight in the test fish in comparison with the control was established. In addition, the feed additive also showed its activity at low ambient temperatures, which allows it to be used on a year-round basis without the risk of reducing its antibacterial activity. Thus, the use of useful probiotic species-specific microorganisms increases the productivity of fish in actively changing environmental conditions, forming a system of sustainable environmental development of aquaculture.