This study was conducted in the Berau Archipelago, East Kalimantan, Indonesia where is indicated as the third highest coral diversity in the world. Main study aim is to understand affects of sedimentation to the coral reef condition using carbon and nitrogen isotope analysis. We analyzed the stable isotopes in both of coral tissue and the zooxanthellae from three coral species, namely Porites spp., Stylophora sp., and Seriotophora sp. A total of 80 coral samples was collected at three localities with two different depths (3m and 10m) from near Berau River mouth to marine area. δ¹³C values of both coral tissue and the zooxanthellae had increased with the distance from the river mouth to marine; -17.8‰ to -8.6‰ and -18.0‰ to -7.4‰ respectively. δ¹⁵N values decreased with the distance from the river mouth which were 6.8‰to 2.3‰ and 5.5‰ to 1.2‰, respectively. In addition, 58 sediment samples were also collected at three lines of the mangrove area at river mouth during dry and rainy seasons. δ¹³C values of sediment in the dry season were higher than rainy season. These results implied that in the rainy season, sediment flow to the coral reefs area was higher than that in dry season and could affect to the coral reef condition, specially for those located close to the river mouth.