Connectivity plays a fundamental role in ecological processes by facilitating the exchange of energy and materials in coastal environments. However, its influence on carbon dynamics within coastal ecosystems remains poorly understood. This study investigates the role of ecological connectivity in affecting sedimentary carbon sources and stocks across a range of interconnected coastal habitats in Berau Coastal Waters, Indonesia, ranging from the transition area to upland vegetation, estuarine mangroves, intertidal mudflats, seagrass meadows, and carbonate mangroves on offshore islands. Sediment samples were collected using a 1-meter-long semi-cylindrical hand auger and were analyzed for elemental and isotopic compositions. A Bayesian isotopic mixing model was applied to estimate the relative contributions of different organic matter (OM) sources to sedimentary carbon. The transition area and mangrove ecosystems exhibited comparable average sediment carbon stocks (~202 Mg C ha⁻¹), higher than those in the intertidal mudflats (151 Mg C ha⁻¹), despite the absence of vegetation in the latter. Mangrove-derived OM contributed approximately 42 - 55% of the sedimentary carbon in the transition area, mangrove ecosystem, mudflat, followed by terrestrial plants-derived OM (26–35%). A declining trend in land-based OM was observed along the land-to-sea gradient, with contributions decreasing from ~37% to seagrass sediment at Rabu-Rabu Island to ~19% at Panjang Island. These findings suggest that both distance from source and hydrodynamic forces (e.g., tides and currents) play key roles in transporting OM across the coastal interface. The Berau coastal system thus functions not only as a carbon sink but also as a carbon transport pathway, linking green carbon from terrestrial sources to blue carbon stored in marine sediments. Recognizing and managing this ecological connectivity is essential for maintaining sediment carbon stocks and has important implications for climate change mitigation and carbon crediting frameworks, especially those requiring deductions for allochthonous carbon inputs.