Lack of a systematic and environmentally efficient approach to exploitation of bays of Sevastopol (Kruglaya and Kazachya bays) resulted in their severe pollution. The combination of natural and anthropogenic factors led to the deterioration of the benthic communities living conditions. The purpose of this work was a complex research of Kruglaya and Kazachaya bays’ ecosystems to study features of redox conditions formation in the bottom sediments and the bottom waters and their influence on the characteristics of macrozoobenthos. Samples of bottom sediments were taken by diver in plexiglass tubes, hermetically closed above and below, it allowed to save a fine structure of bottom sediments and the bottom layer of water. To study benthic communities, samples were taken in the same place using a manual sampler. To obtain the chemical composition of pore waters with high vertical resolution, the voltammetry analysis was used. Calculation of the oxygen flux at the boundary and in the upper part of the bottom sediments was carried out according to the vertical profile of oxygen concentration in pore waters and geochemical analyzes using the equation for the first Fick law taking into account the concentration gradient and molecular diffusion of oxygen in pore waters. Standard hydrobiological methods were used for the analysis of benthic material. When calculating the values of the Shannon diversity index (H'), the base 2 logarithm was used. The data analysis showed that a high level of anthropogenic impact and restricted water dynamics led to siltation of the bottom sediments of the investigated water areas, which made it difficult for oxygen penetration, and the accumulation of organic carbon contributed to its active consumption. Stratification of the water column due to limited water exchange, high temperature of the bottom waters, accompanied by a decrease in oxygen solubility, and finely dispersed nature of bottom sediments contributed to the fact that the rate of oxygen intake was lower than the rate of oxygen consumption for the oxidation of organic matter, which was accompanied by the development of oxygen deficiency zones and the appearance of reduced compounds, in particular hydrogen sulfide. It was noted that suboxic conditions prevailed in the upper layer of bottom sediments, and anaerobic conditions prevailed below. This had led to the fact that the main forms of macrozoobenthos were species tolerant to oxygen deficiency and organic pollution. Thus, in some parts of the Kazachaya Bay were marked only polychaetes. At the same time, it was noted that in the area of exit from Kruglyaya Bay, intense water dynamics and morphological features of the bottom sediments contribute to saturation of the upper layer of sediments with oxygen. Based on the oxygen concentration data in the surface (0 - 5 mm) sediment layer (pore water), and the geochemical composition of bottom sediments, the oxygen flux at station 4 was calculated. Its value was 0.73 M·m-2·year-1. Taking into account the concentration of oxygen in the bottom layer of water (259 μM), the time for complete exhaustion of oxygen or its renewal taking into account only biogeochemical processes was about 5 months. Thus, it can be assumed that the ecosystems of the Kruglaya and Kazachaya bays are in the stage of degradation. Its further exploitation without a developed systematic approach and rational use will lead to a critical deterioration of its ecosystem - the emergence and spread of environmental risk zones. This will reduce the recreational and socio-economic attractiveness of these areas.