Coastal ecosystems produce and sequester significant amounts of carbon (“blue carbon”), which has been well documented in humid and semi‐humid regions of temperate and tropical climates but less so in arid regions where mangroves, marshes, and seagrasses exist near the limit of their tolerance for extreme temperature and salinity. To better understand these unique systems, we measured whole‐ecosystem carbon stocks in 58 sites across the United Arab Emirates (UAE) in natural and planted mangroves, salt marshes, seagrass beds, microbial mats, and coastal sabkha (inter‐ and supratidal unvegetated salt flats). Natural mangroves held significantly more carbon in above‐ and belowground biomass than other vegetated ecosystems. Planted mangrove carbon stocks increased with age, but there were large differences for sites of similar age. Soil carbon varied widely across sites (2–367 Mg C/ha), with ecosystem averages that ranged from 49 to 156 Mg C/ha. For the first time, microbial mats were documented to contain soil carbon pools comparable to vascular plant‐dominated ecosystems, and could arguably be recognized as a unique blue carbon ecosystem. Total ecosystem carbon stocks ranged widely from 2 to 515 Mg C/ha (seagrass bed and mangrove, respectively). Seagrass beds had the lowest carbon stock per unit area, but the largest stock per total area due to their large spatial coverage. Compared to similar ecosystems globally, mangroves and marshes in the UAE have lower plant and soil carbon stocks; however, the difference in soil stocks is far larger than with plant stocks. This incongruent difference between stocks is likely due to poor carbon preservation under conditions of weakly reduced soils (200–350 mV), coarse‐grained sediments, and active shoreline migration. This work represents the first attempt to produce a country‐wide coastal ecosystem carbon accounting using a uniform sampling protocol, and was motivated by specific policy goals identified by the Abu Dhabi Global Environmental Data Initiative. These carbon stock data supported two objectives: to quantify carbon stocks and infer sequestration capacity in arid blue carbon ecosystems, and to explore the potential to incorporate blue carbon science into national reporting and planning documents.