Karst processes-related carbon cycle, as a result of the water–carbonate rock–CO2 gas–aquatic organism interaction, significantly affects global carbon budget. In karst areas, soil CO2 is a major chemical driving force for the karst processes and has significant impact on the geochemical processes of the water–rock–gas–organism system. Currently, there have been many studies mainly focusing on the hydrochemical responses of the epikarst water system to weather conditions. However, few studies examine the direct correlation between the hydrochemical parameters in epikarst systems and soil CO2. We chose an epikarst spring system at Chenqi, Puding, SW China to monitor both the concentration of soil CO2 and hydrochemical parameters at high-resolution (every 15 min) during July 2010–December 2011 covering a complete hydrologic year, and to investigate the response of hydrochemical changes to soil CO2 and weather conditions. It was found that both soil CO2 and rainfall are the major driving forces for the epikarst hydrochemical variations. The soil CO2 effect on hydrochemical variations was reflected in all seasonal, diurnal and storm-scales. There was an increase in pCO2 and electrical conductivity (EC) but a decrease in pH caused by the increase in soil CO2 in spring-summer growing season, while a decrease in pCO2 and EC but an increase in pH caused by the decrease in soil CO2 happened in autumn–winter dormant season. Similar variations were also found on diurnal scales but with a time lag of a few hours between hydrochemical changes and soil CO2 change during dry season, showing effect of the groundwater recharge mode as well as the complexity of the supply path (quick flow by conduit or slow flow by fracture). During rainy seasons, however, hydrochemical changes in epikarst groundwater were regulated by both dilution and soil CO2 effects. Under high-intensity rainfall, the dilution effect was dominant, indicated by a quick decrease in EC, pH and calcite saturation (SIc) but a quick increase in pCO2. In contrast, under low-intensity rainfall, the soil CO2 effect was dominant, indicated by an increase in EC and pCO2 but a decrease in pH and SIc. To sum up, this study has shown the high sensitivity and variability of epikarst processes to the environmental change, implying that the role of karst processes in the global carbon cycle needs to be reappraised based on high-resolution monitoring strategy.