Surface (30 cm) sediment organic carbon (SOC) stock estimated on the South Andaman Island showed the highest value in mangroves during the three seasons i.e., Pre-monsoon (PM), Southwest monsoon (SWM), Northeast monsoon (NEM) covered, compared to the other three distinct blue carbon ecosystems, namely, seagrass, tidal marsh, and seaweed. The annual mean SOC stock was the highest in mangroves (86.58 ± 26.40 Mg ha−1). The highest SOC content and stock in all ecosystems were observed during the NEM followed by the SWM and pre-monsoon. ANOSIM revealed significant seasonal variation (P < 0.02) in SOC stock. The stock declined significantly during the pre-monsoon season, but increased slightly at the beginning of the SWM. Despite the contradictory response of SOC to salinity, the current study indicated that low salinity circumstances linked to NEM rains enhance SOC levels. Pairwise analysis suggested significant variations in SOC between the three seasons (<0.03) indicating that SOC stock in the top 30 cm is inherently unstable on a seasonal scale and hence unlikely to act as a long-term carbon sink. Considering seasonal changes in SOC stocks, a detailed investigation is needed to understand the influence of salinity and other environmental parameters on the carbon storage potential, which would provide new insights into blue carbon dynamics.