<p>This study investigates the role of seagrass habitats in carbon sequestration by quantifying sediment carbon and seagrass coverage in Bahrain’s coastal waters. Recognised as significant carbon sinks, seagrass ecosystems are crucial for marine biodiversity and climate change mitigation. The study uses a twofold approach: assessing sediment carbon content variation across sampling points and estimating seagrass cover with remote sensing techniques using Sentinel-2 and Landsat 8 data. The accuracy of remote sensing-based models for estimating sediment carbon in seagrass is evaluated. Findings show higher sediment carbon concentrations in southern sites and an increase in average sediment carbon content in 2019, despite declines in seagrass coverage and stored sediment carbon. The Landsat 8-based model proved more accurate than the Sentinel-2-based model. This research highlights the importance of preserving seagrass habitats for carbon sequestration, contributing valuable data to global blue carbon reservoirs and informing future conservation strategies and climate change mitigation efforts.</p>