Mangrove ecosystems play a critical role in coastal resilience and long-term carbon storage, yet their spatiotemporal dynamics in small island systems remain poorly understood. This study analyzes mangrove land-cover change from 2000 to 2022 across four major islands in the Karimunjawa Archipelago (Karimunjawa, Kemujan, Parang, and Nyamuk) and projects future trends to 2042. Using multi-temporal satellite imagery and carbon stock–based estimates of CO₂ emissions resulting from mangrove land-cover change, the results reveal heterogeneous trajectories of degradation and recovery. Estimated CO₂ emissions were calculated by multiplying the change in carbon stock, the molecular weight conversion factor from carbon (12/44), and the area of mangrove land-cover change (ha). In 2015, Karimunjawa and Kemujan maintain the largest mangrove extents but are also associated with the highest estimated CO₂ emissions, reaching 273,899.30 t CO₂ ha-¹ as a consequence of land-use conversion, whereas Nyamuk exhibits relatively stable dynamics with localized carbon stock loss corresponding to estimated CO₂ emissions of up to 1,037.13 t CO₂ ha-¹, and Parang shows persistent decline with estimated CO₂ emissions of up to 587.97 t CO₂ ha-¹. Future projections indicate increasing carbon stock loss and associated estimated CO₂ emissions toward 2042, particularly on Kemujan, Nyamuk, and Parang, reaching 574,188.40, 2,551.95, and 1,953.84 t CO₂ ha-¹, respectively, highlighting growing risks to coastal ecosystem integrity and climate change mitigation efforts. These findings underscore the influence of geomorphology, anthropogenic pressure, and governance in shaping mangrove dynamics on small islands. Integrated, site-specific, and adaptive management strategies are therefore essential to conserve mangrove carbon stocks, minimize carbon losses associated with land-cover change, and strengthen coastal resilience in the Karimunjawa Archipelago.