We evaluated the contribution of biological effects (photosynthesis, respiration, and decomposition) to the carbonate parameters and air-water CO₂ fluxes in Tokyo Bay, Ise Bay and Osaka Bay in Japan. The carbonate parameters were measured mainly by cargo ships travelling between Japan and other countries. We used the measurement data from three inner bays and surrounding outer bays in Japan along with reference data from previous studies for complementary analysis. We found that 1) the inner bays in this study were strong annual atmospheric CO₂ sinks, 2) the annual biological effect on the air-water CO₂ fluxes was about 5-25% of the measured CO₂ fluxes and it affected the seasonal variation of the CO₂ flux, and 3) the biological effect was largest in Tokyo Bay, and almost the same in Ise and Osaka Bays. The intensity of the biological effect corresponded mainly with nutrient concentrations, which seemed to be controlled by the wastewater treatment in urbanized areas around the bays. The CO₂ flux was also affected by the seawater residence time, salinity, and stratification. Our results suggest that labile carbon/nutrient ratio of wastewater should be a major consideration for evaluating the biological effect on the carbon cycle in urbanized inner bays, which will continue to expand globally.