An assessment of the hydrochemical parameters and the abundance of the bacterial complex was carried out in the water of a cage farm in the Yaroslavl region in spring 2022, followed by the isolation and identification of cultivated isolates. Ten adult rainbow trout (Oncorhynchus mykiss), aged 2+, which were in a state of physiological dormancy, were studied. An assessment of the microbial contamination of the skin, internal organs and feces was given. The taxonomic diversity of the skin microbiome and immunophysiological parameters of blood were studied. A low number of microorganisms was revealed in the environment. Bacteria of the Aeromonas-Pseudomonas complex of the cage part of the reservoir are opportunistic pathogens and, under stressful conditions, can lead to an outbreak of bacterial infections. Despite the low values of the microbial contamination of the reservoir, the contamination of the digestive tract and excretory system was revealed. Opportunistic bacterial species posing a potential danger to fish have been found in the skin microflora of Oncorhynchus mykiss. The study of indicators of respiratory function and natural blood resistance of commercial trout, age 2+, under farm conditions, indicates chronic exhaustion of the organism and suppression of humoral and cellular immunity factors. Further monitoring of changes in the ecological situation and the sanitary and epizootic state of the reservoir is necessary, which will allow timely measures to be taken to correct the composition of the fish microbiome.