The ecological state of the Sevastopol Bay and the Yuzhnaya Bay is compared by their trophic level using the E-TRIX index. E-TRIX is defined by four state variables, which are strongly correlated with primary production: chlorophyll a, oxygen as absolute % deviation from saturation, dissolved inorganic nitrogen, and total phosphorous. The annual dynamics of biogenic elements is calculated; the one-dimensional water quality model, which has been calibrated for the referred water areas, is used. The annual E-TRIX index variations in the bays are compared; the correlation coefficients between E-TRIX and its parameters are calculated; the contributions of E-TRIX variables are estimated.The annual variation of biogeochemical parameters in the Sevastopol and Yuzhnaya bays has been simulated and E-TRIX index has been estimated. The calculations have showed that on the average the Yuzhnaya Bay has higher trophic level: the average E-TRIX index equals 4.47. In the Sevastopol Bay, the average E-TRIX value equals 4.01. The maximum values of the index have reached 5.53 for the Yuzhnaya Bay and 4.55 for the Sevastopol Bay. However, when the level of phosphates concentration which are the main limiting nutrient elements in the Sevastopol Bay is higher than in the Yuzhnaya Bay (from early July to middle August), the trophic index in the Yuzhnaya Bay is lower than in the Sevastopol Bay.The relative contribution of components in the E-TRIX index has been estimated. It has been revealed that the main factor determining the trophic level in the Sevastopol and Yuzhnaya bays water is the concentration of dissolved inorganic nitrogen. The contributions of the other components in the E-TRIX index are equivalent.