Eutrophication stands out as a primary concern for the Baltic Sea, predominantly attributed to the influx of nutrients, specifically nitrogen and phosphorus, originating from fertilisers. An endeavour was undertaken to evaluate the impact of fertiliser emissions on eutrophication in the Baltic coastal zone, gauged through pollutant concentrations during the period spanning 2010 to 2020. Two-way joining cluster analysis is used to indicate similarities in terms of the highest fertiliser load, by year and country and the semi-Markov model of eutrophication process is applied to both identifying and predicting the degree of eutrophication within the estuaries of seven major Baltic Sea rivers. During the investigated period, Poland and Denmark emerged as the countries with the highest fertiliser use per unit area. Based on the research, it was also determined that the area of the Gulf of Finland, at the mouth of Neva, is the most threatened by eutrophication. This is due to the simultaneous and prolonged occurrence throughout the year of high concentrations of nitrogen and phosphorus compounds in marine water in this region. The relationship between fertiliser use and concentration of nitrates and phosphates in estuaries is also shown.