Rising ocean temperature impacts the functionality and structure of ecosystems, further triggering the redistribution of biodiversity. Still, the magnitude and anticipated impacts of ocean warming are not expected to be uniform across marine space. Here, we developed a two-fold index-based approach to provide an integrated climatic vulnerability assessment of the marine surfaces which are enclosed within protected areas in the Mediterranean Sea. We first built a climatic stability index, based on metrics of analog-based velocity of climate change over a 120-year period (1950-2069), to assess patterns of climate dynamics within the marine protected surfaces. To provide a vulnerability ranking of protected surfaces under climate change, we combined this climate-related index with an index of community stability, reflecting the projected distribution shifts of 71 species of high conservation value. Our analyses revealed a highly heterogeneous and dynamic climatic space, with increasing but spatially inconsistent patterns of climate change velocities over successive 30-year periods. We found that about 62% of the protected marine surface might be subjected to low/very low climatic stability. About 70% of the protected waters were also found to be of limited community stability. Thus, protected surfaces across the Mediterranean basin were characterized by high vulnerability under changing climatic conditions, while only 5.7% of them exhibited high and very high stability based on both indices. Our findings suggest that combining information on climate change dynamics and biotic stability could offer spatially explicit insights which cannot be obtained based simply on the ecological dimensions of conservation planning.