The ecological state of the marine shallow water ecosystem (the case of the Sevastopol Bay) is analyzed by the ratio of assimilative capacity and E-TRIX index depending on the anthropogenic load level for the whole bay ecosystem. As part of analysis, the eastern, central, western parts of the bay were distinguished as well as the Yuzhnaya Bay (southern part). Calculations of the assimilative capacity and E-TRIX index for ecosystems of different parts of the Sevastopol Bay were performed using the in situ data of inorganic nitrogen for the period 1998–2012 obtained from the MHI RAS oceanographic data bank. The paper compares values of ecosystem assimilative capacity calculated for inorganic nitrogen as a prevailing pollutant in municipal and storm wastewaters and E-TRIX trophic index of the sea ecosystem, with the technogenic load and biological process seasonality (warm and cold periods) of nutrient income taken into account. This allowed to properly distinguish water areas, which are most vulnerable in terms of formation of negative ecological events, up to disasters. According to the obtained data, such an area is that of the Yuzhnaya Bay. The second vulnerable water area is the eastern apex part of the Sevastopol bay exposed to the Chernaya River discharge. As the results showed, the situation worsens during winter and spring freshets due to increase in content of inorganic nitrogen forms in the Chernaya River runoff. The ecosystem of the western bay part adjoining the open sea is the safest in terms of nitrate nitrogen assimilative capacity, whereas the central part ecosystem appears to be the cleanest in terms of E-TRIX. The ecosystem most exposed to ecological risks in terms of both indices (assimilative capacity and E-TRIX) is that of the Yuzhnaya Bay (the southern part of the Sevastopol Bay). The observed imbalance of distribution of the calculated trophic index E-TRIX and assimilative capacity in different parts of the Sevastopol Bay is due to various nature of these quantities. The assimilative capacity of an ecosystem is defined by physical, chemical and biological processes given a dynamic removal of pollutants from the ecosystem, whereas E-TRIX is determined, in general, by seasonal variability of nutrient income into the ecosystem.