This model study investigates summer hydrographic changes in response to climate projections following the CMIP5 RCP8.5 scenario. We use the high resolution regional coupled ocean–sea ice–atmosphere model RCA4–NEMO to downscale an ensemble of five global climate projections with a main focus on the Baltic Sea and neighboring shelf basins to the west. We find consistently across the ensemble a northward shift in the mean summer position of the westerlies at the end of the twenty-first century compared to the twentieth century. Associated with this is an anomalous precipitation pattern marked by increased rainfall over northern Europe and dryer conditions over the continental central part. In response to these large-scale atmospheric changes, a strong freshening mainly resulting from a higher net precipitation over the year combined with higher annual mean runoff is registered for the Baltic Sea and adjacent seas. The strongest freshening takes place in the southern Skagerrak region where stronger winds enhance the cyclonic circulation and by this, recirculation of fresher waters from the Baltic Sea strengthens. In the Baltic Sea freshening leads to a reduction in basin averaged salinities between 0.6 and 2.3 g kg−1 throughout the ensemble. Likewise, the sea surface temperature response in the Baltic Sea varies between + 2.5 and + 4.7 K depending on the applied global model scenario. The climate induced changes in atmospheric forcing have further consequences for the large-scale circulation in the Baltic Sea. All ensemble members indicate a strengthening of the zonal, wind driven near surface overturning circulation in the southwestern Baltic Sea towards the end of the twenty-first century whereas the more thermohaline driven overturning at depth is reduced by ~ 25%. In the Baltic Proper, the meridional overturning shows no clear climate change signal. However, three out of five ensemble members indicate at least a northward expansion of the main overturning cell. In the Bothnian Sea, all ensemble members show a significant weakening of the meridional overturning. The entire ensemble consistently indicates a basin-wide intensification of the pycnocline (9–35%) for the Baltic Sea and a shallowing of the pycnocline depth in most regions as well. In the Baltic Sea, which is dominated by mesohaline conditions under the historical period, the changes in salinity at the end of the twenty-first century have turned wide areas to be dominated by oligohaline conditions as a result of climate change. Potential consequences for biogeochemical conditions and implications for biodiversity are discussed.