The global carbon cycle, one of the important biogeochemical cycles controlling the surface environment of the Earth, has been greatly affected by human activity. Anthropogenic nutrient loading from urban sewage and agricultural runoff has caused eutrophication of aquatic systems. The impact of this eutrophication and consequent photosynthetic activity on CO2 exchange between freshwater systems and the atmosphere is unclear. In this study, we focused on how nutrient loading to lakes affects their carbonate system. Here, we report results of surveys of lakes in Japan at different stages of eutrophication. Alkalization due to photosynthetic activity and decreases in PCO2 had occurred in eutrophic lakes (e.g., Lake Kasumigaura), whereas in an acidotrophic lake (Lake Inawashiro) that was impacted by volcanic hot springs, nutrient loading was changing the pH and carbon cycling. When the influence of volcanic activity was stronger in the past in Lake Inawashiro, precipitation of volcanic-derived iron and aluminum had removed nutrients by co-precipitation. During the last three decades, volcanic activity has weakened and the lake water has become alkalized. We inferred that this rapid alkalization did not result just from the reduction in acid inputs but was also strongly affected by increased photosynthetic activity during this period. Human activities affect many lakes in the world. These lakes may play an important part in the global carbon cycle through their influence on CO2 exchange between freshwater and the atmosphere. Biogeochemical changes and processes in these systems have important implications for future changes in aquatic carbonate systems on land.