Mercury biogeochemistry is highly complex in the aquatic ecosystems and it is very difficult to predict. The speciation of mercury is the primary factor controlling its behavior, movement, and fate in these systems. The fluctuating water levels in wetlands could play a major role in the mercury transformations and transport. Hence, the agricultural wetlands may have a significant influence on the global mercury cycling. Kuttanad agricultural wetland ecosystem is a unique one as it is lying below the sea level and most of the time it is inundated with water. To understand the mobility and bioavailability of Hg in the soils of this agricultural wetland ecosystem, the present study analyzed the total mercury content as well as the different fractions of mercury. Mercury was detected using cold vapor atomic fluorescence spectrophotometer. The total mercury content varied from 0.002 to 0.683mg/kg, and most of the samples are having concentrations below the background value. The percentage of mercury found in the initial three fractions F1, F2, and F3 are more available and it may enhance the methylation potential of the Kuttanad agroecosystem.