The intense anthropological impact on the ecosystems makes it necessary to monitor the state of populations of different fish species from different points of view. Health of aquatic animals, including fish, is an informative indicator of the quality of the environment, since physical and chemical changes in water, if they go beyond the optimum, cause definite reactions in the fish body. There are summarized the results of studying the kidneys of cyprinid fish species from the natural habitats of the lower reaches of the Volga and Kigach rivers and the Northern Caspian, as well as those cultivated in pond farms. The detected violations of mesonephros were described depending on localization of the pathological process. It has been shown that pathological changes are found in all structures of the kidney: in the interstitial, renal corpuscle, convoluted muscles. A change in the rheological properties of blood, glomerular changes up to atrophy of capillary loops, dystrophic changes in the tubular epithelium were found. An original system for assessing the condition of fish kidneys is proposed. Reactions in the body of hydrobionts are a consequence of the combined effects of environmental factors and natural physiological processes. The changes detected in the organ structure make it possible to assess the environmental impact on fish. Histopathological changes in vital organs, in particular, in mesonephros, are valuable indicators for assessing the consequences of negative environmental influences. Using not only qualitative, but also quantitative characteristics of mesonephros can contribute to introduce the quantitative methods in ecological and morphological studies of fish.