The present study focus the variation of carbon concentrations within three trophic level i.e., primary producer (phytoplankton), primary consumers (zooplankton) and secondary consumers (fish) in three selected ponds at East Kolkata Wetland area. Depending on the amount and frequency of wastewater input, physico-chemical characteristics of pond, species richness, predator-prey interactions and pond wise different piscicultural practices, the amount of carbon sequestration varied spatially. Significant temporal variations were also observed in each trophic level of these three selected East Kolkata Wetland pond ecosystems. On average primary producers were sequestered 2038.6 ± 244.8mg C m-3 d-1 whereas 307 ± 19.3 mg C m-3 and 11531.4 ± 318.2mg C m-3 was sequestered by primary and secondary consumers, respectively. In Kolkata and its nearby districts over 90% of the production was marked from the East Kolkata Wetland area. Consequently, a significant amount of sequestered carbon was exported from the East Kolkata Wetland ecosystem in the form of fish and this continuous system might increase the carbon sequestration efficiency of the aquatic ecosystem.