Mangrove ecosystems play a crucial role in the global carbon cycle. However, the carbon fluxes in the mangrove ecosystems found in the Indian subcontinent are not well understood. Here, for the first time, we estimate the net ecosystem exchange (NEE) in a mangrove ecosystem at Pichavaram, southeast India, using the eddy covariance method for the period October 2017–September 2018. The half-hourly daytime NEE varied from-11.05 μmol m2 s1 in the winter months (January–March 2018) to-6.06 μmol m2 s1 during the summer (April 2018). The estimated annual evapotranspiration during the study period was 610 mm, whereas the precipitation was 653 mm (much dryer than the long-term average). The half-hourly NEE data were gap filled and partitioned to estimate the gross primary productivity (GPP) and ecosystem respiration (Reco). The estimated annual GPP was 1466 gC m2 and Reco was 1283 gC m2. The mangrove forest appeared to be a modest sink of atmospheric CO2, with an annual average net ecosystem productivity of 183 gC m2. However, in the summer months, it acted as a source. We observed that the mangrove CO2 fluxes strongly responded to environmental factors such as temperature, rainfall, and salinity. However, it is noteworthy that the carbon sink capability may decline in the future due to rising temperatures, decreasing rainfall patterns, variation in salinity, and changes in tidal inundation patterns.