Honda Bay is considered as one of the mercury hotspots in the world due to its proximity to the abandoned Palawan Quicksilver Mine. In this study, a detailed sediment sampling conducted in between 2021 and 2022 where a total of 166 sediment samples were collected along the coast and analyzed for total mercury (THg) concentration. The study assessed mercury toxicity using the geoaccumulation index and compared Hg levels to sediment quality guidelines. The findings revealed a wide range of THg concentrations, from 0.0040 to 11.4702 mg/kg, with hotspots identified at the Honda Bay wharf and Tagburos River mouth. Mercury spreads to a large coastal area brought by tidal currents and the wave energy actions. The geoaccumulation index indicated moderate to strong Hg contamination in the vicinity of the hotspots and around 24.7–36.1 % of samples exceeded the sediment quality guidelines suggesting adverse biological effects in aquatic biota will frequently occur.