As the urgency to reduce carbon emission increases, seagrass ecosystems have recently received attention due to their capacity to take up and store high amounts of carbon. Protection of this ecosystem is key to increase resilience to climate change. However, in some of the Marine Protected Areas (MPAs), seagrass ecosystems are still under threat. This study aims to investigate the current condition of seagrass ecosystems and compare it to the previous study before MPA was established in the Berau coastal water. SeagrassWatch method was used to measure seagrass community structure. Other proxies were also used to explain factors affecting seagrass condition such as Total Suspended Solid (TSS) and sedimentary stable isotopes to identify the source of organic carbon. The percentage cover of seagrass in this study were categorized as not healthy (<29-59,9%), which was statistically related to TSS. The higher TSS resulted in the lower seagrass cover, as observed in the Rabu Rabu island located adjacent to mainland. Changes in seagrass composition were observed, including the emergence of larger species of E. acoroides and T. hemprichii in the islands located adjacent to mainland. The spatial and temporal changes of seagrass ecosystems observed in Berau MPA should be taken into consideration that conservation on seagrass ecosystems needs to be prioritized by improving the MPA function to avoid further loss of carbon from seagrass ecosystems.