Both extreme rainfall events and land-use conversion have increased substantially in recent decades, but their combined effects on the carbon sink function of inland waters are poorly estimated. Based on high-frequency measurements from five karst groundwater–surface water systems in a simulation test site during 2023, we analyzed the dynamics of the carbon sink function of water bodies with different land-use types during precipitation events. The results showed that land surface land-use patterns significantly affected the recovery time of the carbon sink function of water bodies after intense precipitation events. A bare rock–dominated water body had the fastest recovery speed of its carbon sink function, around four times higher than grassland, followed by shrubland, bare soil, cropland, and grassland. The results also showed that precipitation events may not increase CO
2 emissions in bare rock and shrubland systems. In contrast, the water bodies controlled by bare soil, cropland, and grassland showed large but short-term increases in CO
2 emissions after precipitation events. We suggest that these differences can be attributed to the coupled control of the carbonate buffering system and biological pump. We applied sensitivity analysis and Monte Carlo simulation to further evaluate the potential influence of precipitation events on the carbon sink function of karst water bodies. The results showed that the water bodies dominated by shrubland and grassland had a strengthened carbon sink function after precipitation events, compared to the bare soil and bare rock systems. These findings emphasize the critical role of land-use management in regulating the carbon sink function of karst inland waters.