Coastal areas have high potential to store carbon from both terrestrial and marine materials due to the interconnectivity among the habitats. We investigated the contributions of the various sources to the sedimentary organic carbon by examining the δ13C, δ15N, %TOC (total organic carbon) and %TN (total nitrogen) of several marine macrophytes, which included three seagrass species: Cymodocea rotundata Ascherson & Schweinfurth, Cymodocea serrulata (R. Brown) Ascherson & Magnus, and Halophila ovalis (R. Brown) J.D. Hooker; three seaweed species: Halimeda macroloba Decaisne, Halimeda borneensis W.R. Taylor, and Halimeda opuntia (Linnaeus) J.V. Lamouroux; and one coral species, Porites sp., over a vertical gradient at Tangkhen Bay, Thailand. The distribution of organisms differed significantly between distances from the shore and seasons (p < .001), with seagrass occupying the area of 150–350 m from the shore, while Halimeda was most abundant from 150 to 400 m from the shore. The %TOC and %TN in the sediment were significantly different along the shore (p < .001), with the highest values at 300 m from the shore where the highest organism variability was recoded. Seagrass and Halimeda played major roles in sediment organic matter and carbon contributions, contributing up to 42% of the sedimentary organic carbon, while allochthonous sources such as ocean and terrestrial sources had lower contributions. This study elucidates the importance of macrophytes as organic carbon contributors to sedimentary carbon storage, especially in small semi‐enclosed bays.