Abstract This research was conducted on August 2022 (east season) and February 2023 (west season) in Jepara waters. There are four types of seagrasses found: Ea (Enhalus acoroides), Cr (Cymodocea rotundata), Os (Oceana serrulata), and Th (Thalassia hemprichii). The analysis results suggest that the Os species has the largest organic carbon stock within seagrass (OCS-Sg), whereas Ea has the lowest. Aside from morphological measures, in this study seagrass shoot density also determined OCS-Sg for each type of seagrass. This study found that OCS-Sg is higher during the east season (26.2±2.81 gCorg m−2) than the west season (11.2±1.78 gCorg m−2). Whereas, organic carbon stock within sediment (OCS-S) is lower during the east season (41.5±0.9 gCorg m−2) and higher during the west season (56.3±0.9 gCorg m−2). During the east and west seasons, Jepara waters act as a CO2 source. However, during the east and west seasons vegetated OCS-S had higher carbon storage (41.9 and 57.2 gCorg m−2) than unvegetated (39.2 and 53.7 gCorg m−2). This is also indicated by the CO2 flux in vegetated which is lower (13.1±4.8 mmol CO2 m−2 d−1) than unvegetated (16.5±4.7 mmol CO2 m−2 d−1) during the east season. On the other hand, vegetated waters have higher CO2 flux (22.7±2.7 mmol CO2 m−2 d−1) in the west season than unvegetated (18.0±2.5 mmol CO2 m−2 d−1), this is related to seagrass shoot density during the west season which is decreasing. These findings lead to the conclusion that seagrass plays an important role for storing and absorbing carbon and storing carbon and store it in seagrass biomass and sediment even though the role of waters returns CO2 back to the atmosphere.