Abstract: The flow rate of the Pingjiang Underground River exhibits rapid fluctuations during rainy seasons, yet the variation patterns of solute transport with flow changes remain unclear. Tracing experiments were conducted in the downstream sinking stream segment (karst conduit) and open-channel segment of the Pingjiang Underground River under different flow conditions. The morphological variations of breakthrough curves were analyzed, and the transient storage model was employed to simulate tracer transport. The variation patterns of model parameters in karst conduits with flow changes were investigated, and comparisons were made between karst conduits and open-channel segments. The results indicate that as flow decreases, the peak concentration gradually declines with increased tailing extent in breakthrough curves, with minor secondary peaks and oscillations in the tail, suggesting that reduced flow velocities may create low-velocity zones or dead zones within karst conduits. In the transient storage model, the dispersion coefficient shows positive correlation with flow, while both main channel cross-sectional area and storage zone cross-sectional area initially increase and then decrease with rising flow, with no clear relationship observed between exchange coefficient and flow. The dispersion coefficient and exchange coefficient in karst conduits are smaller than those in open-channel segments, whereas the storage zone proportion, main channel cross-sectional area, and storage zone cross-sectional area in karst conduits are significantly larger than those in open-channel segments. These findings provide valuable insights for predicting pollutant transport in karst underground rivers.