Ebrie lagoon is one of the largest in the West Africa lagoon system and contributes to the social and economic well-being of the habitants. Whereas, the sectors IV and V of Ebrié lagoon are increasingly threatened by potential toxic elements (PTEs) pollution due to urban growth, and industrial and agricultural activities, but few studies have focused on the contamination of sediments by PTEs and the human health risks. In the present study, surface sediments from sectors IV and V of Ebrié lagoon were sampled for the geochemical, human risk and ecological risks assessment of four potential toxic elements (PTEs) (As, Cd, Hg and Pb). Results indicate that particle of grain size of > 63 µm (sand) were the most abundant in the surface sediments with relative high TOC content. However, particle size did not affect metals distribution in sediments. PTE mean concentrations did not exceed the UCC values. The geoaccumulation index and enrichiment factor values indicate that no Cd and Pb contamination has occured on the whole, but sediments have been polluted by As and Hg and suggest that Cd and Pb were influenced by from natural weathering processes, whereas As and Hg derived from anthropogenic inputs. The concentrations of Hg higher than PEC, which suggest that it may pose adverse effects to organisms. The results of this study indicated that As, Hg and Pb increase health risks via sediment ingestion for both chidren and adults. With regard to concentrations and level of risk, Hg is the most toxic metal that requires special attention including monitoring of pollution level, wastewater treatment for better environmental management in sectors IV and V of Ebrié lagoon.