Transformations among different mercury species associated with sediments can have a major effect on the metal's mobility and potential for methylation and hence bioaccumulation. In the present study, various fractions of mercury in the sediments of Vembanad wetland system analysed. Total mercury (THg) concentration in the surface sediment varied from 16.3 to 4,230 ng/g. The results of sequential extraction showed that the major portion of mercury in these sediments existed as elemental form followed by organo-chelated form. The least portion observed was the residual fraction (mercury of natural origin). Even though the percentage of mercury observed in the easily available fractions is relatively small, absolute values of these mobile Hg fractions are quite high due to the very high total mercury values. The fractionation of mercury in the sediment was controlled by the organic matter, sulphur complexes and concentration of THg. The results showed that the bioavailability of mercury is high as the amount of mercury found in the initial three fractions is high, which can also enhance the methylation potential of the Vembanad wetland sediments. The fractionation pattern of mercury also revealed the presence of anthropogenic mercury content in the Vembanad wetland sediments.