ABSTRACTEpikarst plays a critical role in karst water circulation, however, its studies have often been limited to small springs or basins, ignoring its importance in larger, highly karstified subterranean streams. This study focused on the Longlingong (LLG) subterranean stream system, where the discharge and electrical conductivity (EC) of the subterranean stream outlet for 2.5 years, and found that 85% of all rainstorm events monitored during this period showed a pattern of increasing and then decreasing EC. High‐resolution hydrochemistry monitoring was conducted at the outlet during a rainstorm event when this response pattern occurred. Simultaneously, epikarst water (EW), saturated zone fissure karst water (FW), and surface water (PW) from this system were collected as three recharge sources for hydrochemical analyses based on the results of the field investigations, and end‐member mixing analyses were performed using the EMMA‐MIX model. These combined methods can accurately characterise the response of the subterranean stream system to rainstorm events, assess the contribution and response of individual recharge sources throughout the rainstorm, and reveal the mechanisms involved. The results indicate that the increase in EC is primarily driven by changes in HCO3− concentration resulting from the rapid discharge of EW through sinkholes and shafts. EW contributes 28.7% of the rain‐induced subterranean stream runoff, exceeding FW. The epikarst exhibits a rapid response to rainstorms, as evidenced by a remarkable 681% increase in EW discharge following a rainstorm event. Flood peaks in the subterranean stream are mainly composed of PW (44%) and EW (43.6%). This study highlights the key role of the epikarst as a karst groundwater reservoir. The sensitivity of the epikarst to rainstorms, particularly its role in facilitating rapid piston‐like migration of EW during initial runoff, highlights its significant influence on discharge and hydrochemistry. This research contributes to a deeper understanding of the function of epikarst within highly karstified subterranean streams.