Seasonal variations in total mercury concentrations [Hg] and trophic transfer through the food web were assessed using stable isotopic tracers for the Setiu Wetlands, Terengganu. The [Hg] measured in surface sediments and biota varied inversely between wet and dry seasons. Increased rainfall and water disturbance during the wet season are suggested as the main factors releasing Hg from surface sediments and enhancing the bioavailability of Hg to biota. The elevated Hg levels associated with the leaf stage suggested that litterfall and atmospheric deposition may be the main Hg inputs into mangrove food webs. The positive relationships between log [Hg] and δ15N provided evidence for Hg biomagnification, however low trophic magnification slopes in both seasons indicated that the ecological risk of Hg in the wetland would be negligible. The [Hg] in fish and commercial crabs were below the permitted limits for human consumption.