The present study collated data on the Indian blue carbon repository (mangroves, seagrasses, and salt marshes) from peer-reviewed literature on carbon stock assessment. This meta-analysis indicated that the blue carbon ecosystems of India could have a collective carbon stock of 67.35 Tg C (mangroves, seagrass, and salt marsh accounting for 67 Tg C, 0.0630 Tg C, and 0.0049 Tg C, respectively). Several studies have ubiquitously measured the spatial extent of mangroves (~ 4991 km2) and seagrasses (~ 517 km2) in India; however, the salt marshes (290–1398 km2) have contradictions in estimates. The green payments against the blue carbon ecosystems of India can be as high as ~ 9.6 billion US $, whereas the social cost of carbon sequestered by these ecosystems can vary between 0.47 and 5.43 billion US $. The present study also identified the key research areas that require priority to minimize the uncertainties in blue carbon stock assessment to foster a robust ecosystem-based approach for climate change adaptation in the country. The study identified that less than half of the total mangrove habitats of India are yet to be sampled leaving a scope of substantial uncertainty in nationwide blue carbon estimates. The spatial extent of India’s salt marshes is another aspect that needs to be delineated with a higher confidence level.