Mediterranean open marine and coastal ecosystems face multiple risks, due to climate change, that impact their unique biodiversity. To assess these risks and evaluate their confidence levels, we adopt the scenario-based approach of the Intergovernmental Panel on Climate Change (IPCC), relying on a review of literature projecting changes in Mediterranean Sea ecosystems. The main drivers of environmental change are sea level rise, ocean warming and acidification. Similar to global conditions, all Mediterranean ecosystems face high risks under all climate scenarios, with coastal ecosystems being more strongly impacted than open marine ecosystems. For these coastal ecosystems, risk levels are expected to become very high already once global warming exceeds 0.8°C with respect to the 1976–2005 period. A few Mediterranean ecosystems (e.g., coralligenous and rocky coasts) have greater adaptive capacity than all others, probably because of the long evolutionary history in this sea and the presence of a variety of climatic and hydrological conditions. Overall, due to the higher observed and projected rates of climate change in the Mediterranean, compared to global trends, for variables such as seawater temperature and pH, marine ecosystems (particularly coastal) are projected to be under higher risks compared to the global ocean.