The difference in accumulation of lead and mercury heavy metals in water, sediments and seagrass organs Enhalus acoroides (roots, rhizomes and leaves) have been found on Kayeli Bay, Buru Island, Maluku. Samples were taken from ten sampling points (Kayeli River Estuary, Suket River Estuary, Anahoni River Estuary, Waelata I Estuary, Waelata River Estuary II, Waeapo River Estuary, Sanleko River Estuary, Marlosso River Estuary, Nametek Beach and Jikumerasa Beach). Pb and Hg were analyzed using Atomic Absorption Spectrophotometer. The content of Pb and Hg in sediments is higher than in the water. The highest Pb and Hg content is found in the roots then in the rhizoma and leaves (roots> rhizoma> leaves). Seagrass (Enhalus acoroides) is one of the living organisms that can be used as a bio-indicator of the level of heavy metal pollution in the aquatic environment