In this study, calculations are performed to reproduce the main components of the Baltic Sea ecosystems based on the stationary, boxed SANBALTS model under various scenarios of climate change in combination with two scenarios of the development of socio-economic conditions. Under various warming scenarios, a decrease in the nutrient load will lead to a reduction in the area of hypoxic zones in the Baltic Sea, while the most significant decrease in the area is due to the scenario of a reduction in the agricultural sector and population. The phosphorus in the benthic layer will decrease, the concentration of inorganic nitrogen will increase, and nitrogen fixation will decrease. The most noticeable decrease in primary production and an increase in water transparency is associated with a moderate climate change scenario and with a significant decrease in the nutrient load. The results showed that under certain combinations of scenarios, an improvement in the ecological state of the sea can be expected even under the most unfavorable climatic scenario.