The Mangunharjo mangrove ecosystem is one of the areas affected by land degradation because of the creation of ponds. This research evaluated the mangrove potential capacity for carbon storage, particularly in absorbing carbon dioxide (CO₂) from the environment. The estimation used allometric equations that employ tree type and diameter at breast height. The carbon content in sediment was also evaluated using the ignition method. Results showed that the estimated value of standing carbon stock in the Mangunharjo mangrove ecosystem is 152.85 ton ha⁻¹. The highest value (i.e., 68.1 ton ha⁻¹) is observed in the area near the river, which is dominated by the Avicennia marina species with a density of 733 ind ha⁻¹. The lowest value (i.e., 34.69 ton ha⁻¹) is observed in the area near the residential area with the A. marina species density of 333.26 ind ha⁻¹. Sediment carbon stocks in all stations amounted to 236.07 ton ha⁻¹. The amount of carbon in sediment is influenced by the sediment type, vegetation type, and sediment age. The total carbon stock in the Mangunharjo mangrove ecosystem is 388.92 ton ha⁻¹, which can be categorized as high potential for environmental services, that is, to absorb CO₂.