The concentration and fluxes of polycyclic aromatic hydrocarbons (PAHs) were investigated in a karst underground river system in southwest China. Groundwater, particles, and sediments from underground river, topsoil, and surface water were monitored, allowing establishment of a conceptual model of PAH transport at the watershed scale. The results showed that PAHs could be transported from the surface to the subsurface through two migration pathways, which were slow-flowing water in the karst fissure and fast-flowing water in conduits. During rainfall events, increasing PAH levels (concentrations and fluxes) at the underground river exit indicated that hydrodynamic force could facilitate PAH transport. The PAHs in water were dominated by dissolved PAHs, accounting for 58.7% of total, especially in the freely dissolved phase, in which SPM-associated PAHs accounted for 41.3% of the total PAHs. Low molecular weight PAHs dominated transport and were mainly transported in dissolved form, whereas high molecular weight PAHs were dominated by SPM-associated transport during the rainfall events. A significantly positive correlation was observed between two-ring and three-ring freely dissolved PAHs and dissolved organic carbon (p < 0.01), respectively. Moreover, PAHs with four to five rings were relatively more abundant in the dissolved organic matter (DOM) associated phase than in the freely dissolved phase, suggesting a major role of DOM in their transport during rainfall events. The trend of PAH fluxes suggested that particle-facilitated transport was another dominant cause of PAH mobilization.