Periphyton that lives attached to seagrass leaves is generally a source of autochthonous energy in the waters and has a major role in the food chain system that supports the primary productivity of seagrass beds. The aim of the current study was to study the extent to which Hg levels affect the ecosystem by looking at Hg accumulation in the periphyton. This study used the method of species composition analysis, the density of epiphytic periphyton algae on seagrass, and analyzed the level of pollution in the Talawan Bajo estuary waters based on the bioaccumulation of mercury (Hg) content in the periphyton and analyzed the periphyton as a bioindicator of the level of Hg pollution in the waters. The first stage was to identify the types of seagrass and periphyton and analyze the composition and density; diversity index, uniformity and dominance of periphyton. The second stage of this study included observation of the accumulation of heavy metal Hg on a laboratory scale and visualization of periphyton cells using TEMcell. Based on the results of the analysis, it was shown that the environmental conditions of the Talawaan Bajo estuary were polluted by heavy metal Hg because the Hg content accumulated in seagrass and periphyton exceeded the quality standards for aquatic biota. It was concluded that the environmental conditions of the Talawaan Bajo estuary were contaminated with heavy metal Hg because the Hg content accumulated in seagrass and periphyton exceeded the quality standards for aquatic biota. Hg contamination in aquatic ecosystems affects the life of biota in the environment, especially damage to tissue structures.