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We developed a three-dimensional model to study the dynamics of carbon dioxide (CO2) emission from a subtropical drinking water reservoir. The quantitative effects of dissolved CO2 concentration on phytoplankton growth were coupled in an inorganic carbon module. Water quality monitoring was carried out to calibrate and validate the model. The simulated surface CO2 concentrations showed no significant difference between seasons (p > 0.05). Regarding the spatial distribution, high CO2 concentrations were observed in the inflow and dam regions (p < 0.05). Four scenarios of different atmospheric CO2 pressures and eutrophic levels were simulated to test the following hypotheses: (1) eutrophication will reverse the carbon budgets in reservoir systems and (2) rising CO2 levels will increase phytoplankton biomass. The results showed that water quality improvements will promote the emission of CO2 into the atmosphere. Simultaneously, the elevated CO2 in the air will stimulate algal biomass, especially in nutrient-rich systems. The systematic analysis of carbon cycling revealed the different internal transformation rates under different scenarios and showed that 32% of carbon was removed via CO2 emission and carbon burial. The interaction provides a novel direction to understand the feedback loops between aquatic ecosystems and increasing CO2 pressure in the future. (C) 2019 Published by Elsevier B.V.