A cross-system analysis of bulk sediment composition, total organic carbon (TOC), atomic C/N ratio, and carbon isotope composition (δ 13C) in 82 surface sediment samples from natural and planted mangrove forests, bank and bottom of tidal creeks, tidal flat, and the subtidal habitat was conducted to examine the roles of mangroves in sedimentation and organic carbon (OC) accumulation processes, and to characterize sources of sedimentary OC of the mangrove ecosystem of Xuan Thuy National Park, Vietnam. Sediment grain sizes varied widely from 5.4 to 170.2 μm (mean 71.5 μm), with the fine sediment grain size fraction (< 63 μm) ranging from 11 to 99.3% (mean 72.5%). Bulk sediment composition suggested that mangroves play an important role in trapping fine sediments from river outflows and tidal water by the mechanisms of tidal current attenuation by vegetation and the ability of fine roots to bind sediments. The TOC content ranged from 0.08 to 2.18% (mean 0.78%), and was higher within mangrove forests compared to those of banks and bottoms of tidal creeks, tidal flat, and subtidal sediments. The sedimentary δ 13C ranged from − 27.7 to − 20.4‰ (mean − 24.1‰), and mirrored the trend observed in TOC variation. The TOC and δ 13C relationship showed that the factors of microbial remineralization and OC sources controlled the TOC pool of mangrove sediments. The comparison of δ 13C and C/N ratio of sedimentary OC with those of mangrove and marine phytoplankton sources indicated that the sedimentary OC within mangrove forests and the subtidal habitat was mainly composed of mangrove and marine phytoplankton sources, respectively. The application of a simple mixing model showed that the mangrove contribution to sedimentary OC decreased as follows: natural mangrove forest > planted mangrove forest > tidal flat > creek bank > creek bottom > subtidal habitat.