Climate observations for the Baltic Sea show a warming of 0.85 °C throughout the last 100 years. Projections for the 21st century indicate an accelerated warming trend and changes in precipitation patterns. These changes could have an impact on the ecological system of the Baltic Sea, as described in the Assessment of Climate Change for the Baltic Sea Basin. This study models these ecological impacts in using a simple ecological model that was applied to the habitat type ‘reefs’ within the marine Special Areas of Conservation (SACs), according to the European Habitat Directive. Based on results from the REMO regional climate model, changes of the ecological system of the Baltic Sea were modelled. Furthermore, the most important reef characteristics and climate factors which induce ecological impacts in the area were identified. Results indicate that the trophic level and light conditions of a SAC determine the direction and the magnitude of climate-induced ecological impacts. The most important climate element was found to be precipitation over land which controls the runoff and, therefore, the nutrient and freshwater input into the ecosystem of the Baltic Sea