Net absorption of CO2 by vegetated coastal ecosystems has been revealed as a key mechanism to capture and store carbon via the renewal of epigeal stem and rhizome biomass. Submerged aquatic ecosystems, such as seagrass meadows, have been termed “blue carbon” ecosystems because they absorb CO2 for their underwater growth. Irradiance and water temperature are significant factors controlling net ecological production (NEP) by seagrass. As seagrass tends to grow in calm coastal areas subject to water-column stratification, such as lagoons, a new method for evaluating NEP accurately to access blue carbon capture in these enclosed waters is required. This study aimed to develop a model to investigate thermal effects, considering irradiance, on changes in dissolved inorganic carbon dynamics in a lagoon system, and assessment of the model to understand controls on carbon dynamics in Komuke Lagoon, Japan. NEP was successfully modelled by verifying its robustness against field observations. Furthermore, the proposed model can be applied to assess and enhance the effectiveness of blue carbon capture and storage as part revegetation measures to mitigate against global warming.