The impact of seasonal coastal upwelling on the dynamics of dissolved inorganic carbon (DIC) and sea-air fluxes of CO2 along the coastal waters of Kochi was investigated during 2015, as a part of Ecosystem Modelling Project. The surface water pCO2 varied from 396 to 630μatm during the study period. Significant inter-seasonal variations were found in the distribution of physico-chemical variables and surface pCO2. An increase of 102.1μatm of pCO2 was noticed over a two-decade period with a rate of 5.3μatmy−1. There was an agreement between the fluxes of CO2 and net ecosystem production (NEP) with respect to the trophic status while NEP was higher than CO2 fluxes by a factor of 3.9. The annual net ecosystem exchange (NEE) was estimated to be 15.02mmolCm−2d−1 indicating that the coastal waters of Kochi are highly heterotrophic in nature.