Description: Eutrophication and climate change will affect habitats of species and more generally, the structure and functioning of ecosystems. We used a three‐dimensional, coupled hydrodynamic‐biogeochemical model to investigate potential future changes in size and location of potential habitats of marine species during the 21st century in a large, eutrophicated brackish sea (the Baltic Sea, northern Europe). We conducted scenario projections under the combined impact of nutrient load and climate change. Possible future changes of the eutrophication state of this sea were also assessed through two policy‐relevant indicators. The results imply a physiologically more stressful environment for marine species by the end of the 21st century: volumes of higher salinity water become more hypoxic/anoxic and the volumes of low salinity, oxic water increase. For example, these results impact and reduce cod reproductive habitats. The decrease is mainly climate change induced in the Baltic basins less directly influenced by inflows of saline, oxic water to the Baltic Sea (E Gotland and Gdansk Basins). In basins more directly influenced by such inflows (Arkona and Bornholm Basins), the combined effect from climate change and nutrient loads is of importance. The results for the eutrophication state indicators clearly indicate a more eutrophic sea than at present without a rigorous nutrient reduction policy, that is, the necessity to implement the Baltic Sea Action Plan. The multidisciplinary, multiscenario assessment strategy presented here provides a useful concept for the evaluation of impacts from cumulative stresses of changing climate and socioeconomic pressures on future eutrophication indicators and habitats of marine species.