Groundwater (GW)-surface water (SW) interactions in karst areas may have a strong impact on the quantity and quality of the groundwater system. Although knowledge of karst hydrology has improved in recent decades, the interaction patterns of GW-SW, and understanding of the hyporheic zone (HZ) on improving or deteriorating groundwater remains very limited. Here, we document HZ in a karst basin through study of hydrological, hydrochemical, and biological processes. The depths of some sinkholes or karst windows in the karst plain are more than 100 m, which are dozens of meters lower than the river elevations. The HZ is not limited to the riverbed, but extends into aquifer along the karst conduits. And their interaction patterns are not limited to the mixing GW and SW, but also include mixing of groundwater with other water bodies. Due to the existence of karst conduits, the types of HZ and the dynamic process of hyporheic flow are unique within karst aquifers. We defined these generally in karst groundwater systems dominated by conduits as karst cave hyporheic zones (KCHZ), with the meaning of the place or area where conduit flow interacts with other types of water bodies. The KCHZ was further classified into four types. Research on the five springs in the study area showed the formation of KCHZ is related to the karst development and the hydrogeochemical gradient of water environment. Once the quality of one type of water deteriorates, or the amount of water decreases, the function of hyporheic zone will degenerate.