Ocean health is critical for human well-being but is threatened by multiple stressors. Parties to the Convention on Biological Diversity agreed to protect 10% of their waters by 2020. The scientific evidence supporting the use of marine protected areas (MPAs) to conserve biodiversity stems primarily from knowledge on fully protected areas, but most of what is being established is partially protected. Here, we assess the protection levels of the 1,062 Mediterranean MPAs. While 6.01% of the Mediterranean is covered by protection, 95% of this area shows no difference between the regulations imposed inside the MPAs compared with those outside. Full and high levels of protection, the most effective for biodiversity conservation, represent only 0.23% of the basin and are unevenly distributed across political boundaries and eco-regions. Our current efforts are insufficient at managing human uses of nature at sea, and protection levels should be increased to deliver tangible benefits for biodiversity conservation.