Understanding groundwater flow and chemical transport is crucial for operating underground storage caverns. Groundwater flow in the study area is mainly affected by cavern operating conditions, and groundwater chemistry in the study area is modified by disinfection activities for removing possible biological clogging and by mixing with cement pore water. It is significant to discern these two effects because wells affected by the disinfection activities, in particular, may have hydrological connections with water curtains in which disinfectant water was injected to remove the biological clogging. Concentration of tritium (3H) and helium isotopes (4He), and groundwater chemical compositions were used to confirm that there are hydrological connectivities between the water curtain and the well. Groundwater along the fault areas contains low total dissolved solid (TDS) and high 3H, suggesting that the faults may act as fast flow conduits, which is not inconsistent with previous studies. Certain diagnostic conditions (high concentrations of Na+, Cl− and TDS and high pH) are presumed by the effect of disinfection activity, indicating that there are hydrological connections between the water curtain and the wells. This hypothesis is valid in YK2U and YK2L, but is not in YK12L, implying a closed system or an immobile water to explain the isotopic results.