<p>Enclosed marginal seas are hotspots of endemic biodiversity that sustain societies through fisheries, tourism, and vital ecosystem services. Their small size makes them highly sensitive to global warming but systematic assessments of future climate change are lacking. Using climate model projections and reanalysis data, we assess two key thermal stressors across 19 seas: the rate of warming that limits the adaptive capacity of ecosystems, and the emergence of near-permanent marine heatwaves. We find these seas have already entered an unprecedented warming phase following the reversal of aerosol cooling effect in the late 20^th century. Under unmitigated future scenarios, many seas would experience climate warming rates three to four times higher than previously observed, with 15 seas at risk of entering near-permanent heatwave states. Limiting global warming to below 2 °C prevents such extremes, but seas still warm substantially: 13 seas exceed &gt;1 °C warming above preindustrial levels, and over 60% of the seas area transforms to a near-permanent heatwave state at mid-century. These findings highlight that even under the most optimistic scenarios, safeguarding the ecological integrity and socioeconomic value of marginal seas demands transformative adaptation, proactive conservation, and large-scale restoration efforts.</p>