Increase in the water area trophic state is one of the unfavourable consequences of anthropogenic impact on the ecological state of the marine environment. The cause of water body eutrophication is often an excessive input of nutrients and easily oxidisable organics, the main source being river runoff and sewage. The main aim of the work is to determine seasonal changes in the trophic state of the Limensky Bay water area based on numerical modelling data. The data required to calculate the trophic state index were derived using a one-dimensional version of the water quality model and its eutrophication block. The annual course of chlorophyll a concentration, nitrate and nitrite nitrogen, ammonium, phosphate phosphorus and oxygen was obtained for the Limensky Bay water area. The trophic state index was calculated from these biogeochemical indicators. The sea water in the study area was of good quality and its state was mesotrophic. Only in the cold period on the 1st–104th and 356th–365th model days, the index was below 4, which corresponds to an oligotrophic state. The maximum index value (4.39) was on the 247th model day and the minimum value (3.82) was on the 365th model day. The best correlation of the trophic state index was observed for the concentration of chlorophyll a (r = 0.84), mineral nitrogen (r = 0.80) and total phosphorus (r = 0.78). The calculated relative contribution of the components, included in the calculated formula of the E-TRIX index, showed that the main factor determining the eutrophication level of Limensky Bay waters was the concentration of mineral forms of nitrogen. This study can be used for monitoring the areas where in situ sampling is difficult.