Blue carbon (BC) ecosystems provide important and multiple ecosystem services, including climate change mitigation through carbon storage. However, these ecosystems are under the pressure of numerous anthropogenic stressors, such as population growth and industrialization, which jeopardize the benefits they provide. Although the common methodology is based on the use of a linear depth scale, this work highlights the need of sediment dating to evaluate temporal variation of organic carbon (Corg) stocks and burial rates, since sedimentation patterns can be variable even between sites within a single ecosystem. Temporal records of Corg stocks and burial rates during the past 100 years were determined in mangrove, seagrass and salt marsh ecosystems, from five representative areas of the Mexican marine coastal systems, by using 210Pb-dated sediment cores. Carbon stocks during the past 100 years (Corg stock(100 years)) ranged from 67 to 269 Mg Corg ha−1 in mangroves, 8–53 Mg Corg ha−1 in seagrasses and 32–56 Mg Corg ha−1 in salt marshes, and burial rates were 8–426 g m−2 yr−1, 2–252 g m−2 yr−1 and 1–60 g m−2 yr−1, respectively. Most of the stored Corg (60–86%) accumulated during the Anthropocene (since 1950), and in mangrove cores recent Corg stocks were up to six times higher than before the Anthropocene onset (1900–1950), most likely as a result of land use changes. Increased Corg burial rates in seagrass ecosystems were mostly driven by mass accumulation rate changes (promoted by catchment erosion and sea level rise), and in mangroves and salt marshes by changes in Corg content, likely promoted by an increase in productivity associated with nutrient enrichment by fertilizer runoff and sewage disposal. Despite the multiple anthropogenic stressors that positively affected Corg stocks and burial rates in BC ecosystems, worldwide destruction of these valuable habitats will cause losses of long-term buried Corg through significant CO2 releases, thus conservation and/or restoration are effective actions for climate change mitigation.