An epidemiological situation was revealed during the period of investigations (2013-2017) at the 10 fish farms in pools in the territory of the Azerbaijan. Totally, 2971 marketable fish were studied by the method of complete parasitological dissection. All fish specimens belonged to 14 species and 4 families (Cyprinidae, Percidae, Siluridae, Poecilidae). The number of identified parasites was 64 species from the 8 systematical groups (Protozoa (14), Monogenea (15), Cestoda (9), Trematoda (13), Acanthocephala (1), Nematoda (7), Annelida (1), Crustacea (4). The species composition of parasites fauna, biology and geographical distribution of marketable fish, effect of environmental factors on the epidemiological situation in fisheries were studied. It should be noted, that farming fishes have diseases, predominantly caused by pathogenic parasitic protozoa and flukes. Gills, intestines, body, cavity and skin were seriously infected. At the same time, diseases caused by bacteria and protozoa are capable of producing major outbreaks in the dramatic changes in environmental conditions. Control measures have been developed to prevent parasitic diseases that may occur when the temperature rises in the summer. The course of treatment is proposed to be carried out integratable by veterinary and sanitary expertise, land reclamation and zootechnics safety precautions. Before the treatment the extensiveness of invasion by bacterial diseases and acanthocephalan species were equal 47% and 58%, respectively. After the full course of treatment Antibac-100 powder and Tetramizole 20% were demonstrated the 100% efficiency. As a result of suggesting therapeutic and prophylactic arrangements, the quantity and weight of fish in fish farms were increased.