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Coastal seagrass, mangrove and salt-marsh ecosystems-also termed blue-carbon ecosystems-play an important role in the global carbon cycle. Much of the organic carbon they store rests in soils that have accumulated over thousands of years. Rapidly changing climate and environmental conditions, including sea-level rise, warming, eutrophication and landscape development, will impact decomposition and thus the global reservoir of blue soil organic carbon. Yet, it remains unclear how these disturbances will affect the key biogeochemical mechanisms controlling decomposition-mineral protection, redox zonation, water content and movement, and plant-microbe interactions. We assess the spatial and temporal scales over which decomposition mechanisms operate and how their effectiveness may change following disturbances. We suggest that better integration of decomposition mechanisms into blue-carbon models may improve predictions of soil organic carbon stores and facilitate incorporation of coastal vegetated ecosystems into global budgets and management tools.