Abstract: Select results from modern karstology research show that carbonate rock can be actively involved in the global carbon cycle with a quick response, thus the carbon sink effect from the water cycle in carbonate rock areas is very important. As described in this paper, three representative karst groundwater systems were selected, including Guangxi province Guilin Zhaidi, Guangxi province Huanjiang county Da'an groundwater and Chongqing Qingmuguan groundwater. Carbon sink flux (CO₂) of each underground water system was estimated from the serial monitoring data of discharges and bicarbonate concentrations by using the simple chemical equilibrium method. The fluxes in Zhaidi, Da'an and Qingmuguan were 68.82 t/(km²·a), 81.18 t/(km²·a) and 100.07 t/(km²·a) respectively. The structures and environmental conditions in each karst water system were relatively stable; accordingly, the groundwater discharge and HCO₃^- concentration were two key factors influencing karst carbon sink intensity, especially the flow rate change of underground streams. However, the carbon sink flux could be controlled by water chemistry and hydraulic conditions and was also impacted by land use change for different karst water systems. The results of carbon sink fluxes from three typical underground water systems provided references for the improvement of the carbon cycle model and the estimation of the karst carbon sink.