An empirical model is developed and used with remotely sensed predictors: sea surface temperature (SST) and chlorophyll-a concentration (Chl-a), to compute surface water partial pressure of carbon dioxide (pCO2w) and air-sea fluxes of CO2 in the Hooghly estuary and its adjacent coastal oceans. In situ observations used here were based on measurements carried out in this region during winter and summer periods in 2008. The estimated pCO2w compares well with the in situ observations at root mean square error ±18 μatm. In winter, estimated pCO2w ranges between 320 and 500 μatm with large values (>400 μatm) on the south-western and south-eastern flanks of the coastal domain and lower values (340–375 μatm) on the main-channel. In summer, it remained spatially uniform at 450 μatm. Extrapolation of the results over the study region based on the Moderate Imaging Specroradiometer (MODIS) measured SST and Chl-a suggests that the region is a strong source of atmospheric CO2 during the summer with net release of 0.095 Tg C year−1 (equivalent to mean flux of 90 molC m−2 year−1) and is a weak source during the winter with net release of 0.006 Tg C yr−1 (0.5 molC m−2 year−1) from the geographical extent of 6000 Km2 area.