The impact of present and future changes in factors which effect the Baltic Sea ecosystem, can only be estimated and predicted if the involved processes are known und understood. Therefore three-dimensional numerical models are tools to provide sophisticated knowledge about these processes with relative slight effort. The main topic of this study is the simulation and statistical analysis of the modern warm period scenario compared to paleo oceanographic scenarios of the last 1000 years. In this study it was shown that the modification of external factors in the paleo oceanographic scenarios influence the whole modelled Baltic Sea ecosystem in a significant way. For instance the salinity changed and therefore the distribution of species along the changed salinity gradient would be changed. Furthermore the ecological important expansion of anoxic and hypoxic areas at the bottom water layer was less distinct as in the modern warm period scenario. Also it was shown that the stratification and therefore the conditions of the water bodies are significant influenced by wind induced ventilation. The comparative examination of the modelled scenarios leads to the conclusion that the nutrient input into the Baltic Sea is the main reason for the spreading of anoxic and hypoxic bottom areas, followed by climate change.