The openness and sensitivity of karst water systems make the geochemical processes of groundwater in karst areas of great importance. In this study, the recharge processes have been identified based on physical-chemical indicators (T, DO, EC, HCO3 −, SO4 2−, Cl-, Na+, Ca2+, and Mg2+), δ2H, δ18O, and δ13CDIC isotopes. The results are as follows: (1) Ions exchange is active in karst groundwater, particularly during the dry season. (2) Evaporation and precipitation are significant but seasonally varied processes governing the recharge of the Lihu underground river. Spring and summer show significant groundwater recharge driven by rainfall, with intense evaporation in summer and the isotopic and d-excess values in autumn reflecting the reduced rainfall and cooler weather. Despite the combined influence of surface water and rainfall in winter, low precipitation produces predominantly old groundwater, resulting in pronounced evaporative effects on groundwater isotopic composition. (3) δ13CDIC values are generally heavy (-10.74‰ to -4.34‰) in the underground water, indicating rapid surface water infiltration with short residence times and abbreviated karstification processes in summer versus longer residence times and prolonged karstification in winter. This study highlights chemical and isotope analysis to understand karst recharge and hydrodynamics in Southwest China and beyond.