Investigasi terhadap kondisi lamun di perairan Teluk Balikpapan telah dilakukan, namun perhitungan stok karbon di sedimen lamun yang berada di perairan estuari tersebut belum tersedia. Penelitian ini bertujuan untuk mengestimasi cadangan karbon pada sedimen lamun di Pulau Kedumpit yang berlokasi di Teluk Balikpapan, Kalimantan Timur. Masing-masing sampel sedimen diambil pada 3 titik stasiun yang berbeda, dengan titik stasiun (0, 50 dan, 100 meter) dari daerah lamun yang dekat dengan dataran menuju ke arah laut. Pengambilan sampel sedimen menggunakan pipa PVC berdiameter 2,5 inch dengan kedalaman sampel 0 – 50 cm dan dipotong dengan interval 5 cm. Kandungan karbon organik dianalisis dengan metode Loss on Ignition (LoI). Hasil studi menemukan terdapat dua jenis lamun yaitu Halodule sp. dan Halophila sp. Berdasarkan visualisasi sampel sedimen bahwa jenis substrat di lokasi penelitian cenderung pasir berlumpur. Konsentrasi karbon organik sedimen pada tiga stasiun berkisar antara 0,34-2,64% dengan rata-rata 1,24±0,37 %. Nilai stok karbon sedimen per lapisan sedimen berkisar 63 hingga 114 MgC/ha dan rata-rata total simpanan karbon sebesar 95±27,6 MgC/ha pada kedalaman sedimen 0-50 cm. Terdapat perbedaan yang signifikan pada nilai bulk density, karbon organik sedimen, dan stok karbon dalam sedimen (p-value < 0,05) antar stasiun dan kedalaman. Seagrass in Balikpapan Bay estuary already investigated, however its carbon stock have not been measured. The objective of this study was to estimate the carbon stock in seagrass sediments in Kedumpit Island, located in Balikpapan Bay estuary. Each sediment sample was taken at 3 different sites (0, 50 and 100 meters) from the seagrass area near to the land towards the sea. Sediment samples were taken using a 2.5 inch diameter PVC core with a depth of 0 - 50 cm and were sliced at 5 cm interval. Organic carbon content was analysed using the Loss On Ignition (LOI) method. Study results showed that two seagrass species were found in the study site, such as Halodule sp and Halophila sp. Based on visual observation at sediment samples, the substrate type in the study site tends to be muddy sand. Sediment organic carbon concentration at three stations ranged from 0.34-2.64%, with average at 1,24±0,37%%. Sediment carbon stock values of sediment layers ranged from 63 to 114 MgC/ha and the total average carbon storage was 95±27,6 MgC/ha. The value of bulk density, sediment organic carbon, and carbon stock in sediment were significantly different (p-value < 0.05) between the sites and the depth of sediment layers.