Mexico has more than 750,000 ha of mangroves and more than 400,000 ha of seagrasses. However, approximately 200,000 ha of mangroves and an unknown area of seagrass have been lost due to coastal development associated with urban, industrial and tourist purposes. In 2018, the approved reforms to the General Law on Climate Change (LGCC) aligned the Mexican law with the international objectives established in the 2nd Article of the Paris Agreement. This action proves Mexico’s commitment to contributing to the global target of stabilizing the greenhouse gas emissions concentration in the planet. Thus, restoring and conserving mangrove and seagrass habitats could contribute to fulfilling this commitment. Therefore, as a first step in establishing a mitigation and adaptation plan against climate change with respect to conservation and restoration actions of these ecosystems, we evaluated Mexican blue carbon ecosystems through a systematic review of the carbon stock using the standardized method of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We used the data from 126 eligible studies for both ecosystems (n = 1220). The results indicated that information is missing at the regional level. However, the average above and below ground organic carbon stocks from mangroves in Mexico is 113.6 ± 5.5 (95% CI [99.3–118.4]) Mg Corg ha−1 and 385.1 ± 22 (95% CI [344.5–431.9]) Mg Corg ha−1, respectively. The variability in the Corg stocks for both blue carbon ecosystems in Mexico is related to variations in climate, hydrology and geomorphology observed along the country’s coasts in addition to the size and number of plots evaluated with respect to the spatial cover. The highest values for mangroves were related to humid climate conditions, although in the case of seagrasses, they were related to low levels of hydrodynamic stress. Based on the official extent of mangrove and seagrass area in Mexico, we estimate a total carbon stock of 237.7 Tg Corg from mangroves and 48.1 Tg Corg from seagrasses. However, mangroves and seagrasses are still being lost due to land use change despite Mexican laws meant to incorporate environmental compensation. Such losses are largely due to loopholes in the legal framework that dilute the laws’ effectiveness and thus ability to protect the ecosystem. The estimated emissions from land use change under a conservative approach in mangroves of Mexico were approximately 24 Tg CO2e in the last 20 years. Therefore, the incorporation of blue carbon into the carbon market as a viable source of supplemental finance for mangrove and seagrass protection is an attractive win-win opportunity.