Uncertainties of projected physical key parameters and ecological quality indicators of the Baltic Sea environment, like water temperature, salinity, oxygen, nutrients and water transparency in future climate are assessed. We analyzed an ensemble of 38 scenario simulations for 1961-2099. Three state-of-the-art coupled physicalbiogeochemical models are forced with four regionalized climate projections assuming either the A1B or A2 greenhouse gas emission scenario and with four nutrient load scenarios covering the entire range from a pessimistic to a optimistic assumption of the future socioeconomic development in the Baltic Sea region. We found considerable discrepancies of projected ecological quality indicators because the sensitivities of the ecosystem response to nutrient load and temperature changes differ among the models. However, despite these uncertainties all three models agree qualitatively well in their overall response. In particular, the impact of warmer water counteracts in all models the impact of nutrient load reductions.