Lagoons of West African countries are seriously threatened by rapid artisanal and small-scale gold mining (ASGM) that exposes lagoons to mercury pollution. In this study, the mercury level in the sediments of the Tendo and Aby lagoons in Côte d'Ivoire had been evaluated. A total of 87 samples from 25 stations located on Tendo and Aby lagoons were analyzed by atomic fluorescence spectrometry. The mean Hg concentrations obtained in the sediments of Tendo and Aby lagoons were 0.89 ± 0.26 mg•kg −1 and 0.70 ± 0.18 mg•kg −1 , respectively. Hg concentrations evaluated in the bays of Tendo and Aby during the dry season were 1.38 ± 0.45 mg•kg −1 and 1.07 ± 0.31 mg•kg −1 , respectively. The minimum and maximum total Hg concentrations in the sediments from 25 stations were 0.04 and 3.56 mg•kg −1 , respectively. Mercury contamination in lagoons during ASGM poses risks of pollution for the lagoon ecosystem and also poses health risks for the population living near these lagoons.