Improved knowledge on the risk in ecologically important habitats on a regional scale from multiple stressors is critical for managing functioning and resilient ecosystems. This risk assessment aimed to identify seagrass ecosystems in southern Sweden that will be exposed to a high degree of change from multiple global change stressors in mid- and end-of-century climate change conditions. Risk scores were calculated from the expected overlap of three stressors: sea surface temperature increases, ocean acidification and wind driven turbid conditions. Three high-risk regions were identified as areas likely to be exposed to a particularly high level of pressure from the global stressors by the end of the century. In these areas it can be expected that there will be a large degree of stressor change from the current conditions. Given the ecological importance of seagrass meadows for maintaining high biodiversity and a range of other ecosystem services, these risk zones should be given high priority for incorporation into management strategies, which can attempt to reduce controllable stressors in order to mitigate the consequences of some of the impending pressures and manage for maintained ecosystem resilience.