It is imperative to understand the carbon (C) and nitrogen (N) pools in tropical mangrove systems considering the diminished C storage potential and increasing nutrient loading in a global context due to rising anthropogenic disturbances. Here, we report that the Mangalavanam Coastal Wetland (MCW), a tropical mangrove stand, is a C-rich environment, with high sediment total organic carbon (70.35 ± 23.84 mg/g) and the δ 13 C (−26.56 ± 0.65‰) signatures indicate that the major source of carbon in the study area is from mangrove litter. The total nitrogen concentration in the sediment (3.78 ± 0.18 mg/g) was high despite the low N environment of mangrove ecosystems where the mangrove leaf litter was a major contributor to C. The sediment δ 15 N (7.70 ± 0.23‰) signatures indicated that the influence of anthropogenic N discharges and the contribution of marine algae were the primary cause of N enrichment. The mean δ 13 C and δ 15 N signatures of the mature mangrove leaves of the MCW were −28.66 ± 1.04‰ and 5.93 ± 0.65‰, respectively. The mangrove dweller crab Parasesarma plicatum was observed to have enriched δ 13 C (−23.78 ± 0.33‰) and δ 15 N (6.54 ± 0.35‰) signatures, indicative of a mixed dietary source. This study provides the impetus for ongoing conservation efforts to limit the loss of carbon storage and protect against the impact of anthropogenic nitrogen loadings on lowering the carbon and nitrogen emission potential for this system, which can have implications for other tropical mangrove systems as well.