Underground rivers serve as a key groundwater storage mechanism in the karst regions of Southwest China. A comprehensive understanding of their structural characteristics and flow pathways is crucial for groundwater resource assessment, protection, and engineering applications. Taking the Pingjiang underground river as a case study, the architecture of karst conduits and flow dynamics were investigated through tracer tests, hydrogeochemical monitoring, and integration of hydrogeological data. The results revealed that the groundwater in the Pingjiang underground river is of the HCO₃-Ca type, with hydrochemical composition primarily shaped by leaching processes. Stable isotope ratios (δD and δ¹⁸O) were found to exhibit a progressive enrichment trend along the flow direction, indicating that water-rock interaction was enhanced and the system confinement in the downstream segment was relatively greater compared to the middle and upper reaches. The Pingjiang system was characterized as a multi-source, single-sink underground river, with dendritically distributed karst conduits comprising one main conduit and four tributaries. The breakthrough curve from the tracer test in the main conduit displayed a distinct “plateau” feature, suggesting the coexistence of well-developed conduits and fractures, as well as the presence of multiple transient storage zones along the flow path. These findings provide valuable insights for the investigation, development, and sustainable utilization of groundwater resources in complex karst aquifer systems.