Carbon capture and storage due to photosynthesis activities has been proposed as a carbon sink to mitigate climate change. To enhance such mitigation, previous studies have shown that freshwater lakes should be included in the carbon sink, since they may capture as much carbon as coastal areas. In eutrophic freshwater lakes, there is uncertainty about whether the equilibrium equation can estimate the partial pressure of carbon dioxide (pCO₂), owing to the presence of photosynthesis due to phytoplankton, and pH measurement error in freshwater fluid. Thus, this study investigated the applicability of the equilibrium equation and revealed the need to modify it. The modified equilibrium equation was successfully applied to reproduce pCO₂ based on total alkalinity and pH through field observations. In addition, pCO₂ at the water surface was lower than the atmospheric partial pressure of carbon dioxide due to photosynthesis by phytoplankton during strong stratification. The stratification effect on low pCO₂ was verified by using the Net Ecosystem Production (NEP) model, and a submerged freshwater plants such as Potamogeton malaianus were found to have high potential for dissolved inorganic carbon (DIC) sequestration in a freshwater lake. These results should provide a starting point toward more sophisticated methods to investigate the effect of freshwater carbon on DIC uptake in freshwater stratified eutrophic lakes.