<p>Karst aquifers are particularly vulnerable to tunnel excavation; however, studies on tunnels in karst environments remain limited, and none have explored the depth and pathways of karst groundwater circulation resulting from tunnel excavation using hydrogeochemical evaluation. This study analyzed hydrogeochemical variations in precipitation, groundwater and tunnel drainage in a karst trough valley in Chongqing, Southwest China, comparing these changes to groundwater levels and discharges. Following tunnel excavation, ion concentrations derived from human activities in epikarst springs decreased, while ion concentrations from natural karst processes increased. At the drainage zone near the exit of the adjacent railway tunnel, the increase in ion concentrations from human activities was greater than the changes in other ions, while ions from karst processes showed a decrease. The evaluation of groundwater discharge and hydrogeochemical changes indicated that tunnel excavation altered the pathways and depths of groundwater circulation. Newly formed fissures generated from the tunnel excavation provided additional runoff pathways for downward movement of upper soil water and epikarst water, resulting in variations in groundwater mixing and changes in hydrogeochemical characteristics. This study provides evidence and a practical approach for investigating groundwater circulation in karst trough valleys.</p>