Thallium is a highly toxic element, whose geochemical dispersion, transfer and potential health risks in aquatic systems are far from understood. This study aims to investigate the distribution of Tl in the surface water from an ultra-large Tl-bearing pyrite open-mining site and its associated riverine system of Yunfu city, western of the Pearl River Basin (PRB). Concentrations of 2.75–194.4 μg/L of Tl were found in the surface water from the mining site. Compared with other trace metals measured (Al, As, Cd, Co, Cr, Cu, Mn, Ni, Pb and Zn), Tl experienced little precipitation by conventional lime-dosing treatment of mine water and readily moved through the river trace. The distribution of Tl in the river watershed during both the dry season (Tl: 0.01–9.15 μg/L) and wet season (Tl: 0.03–1.92 μg/L) generally followed a decreasing concentration pattern downstream of the pyrite mining site for the upper and middle reaches. However, some unexpected Tl elevations were observed in the lower reaches. Concentrations of Tl correlated well with concentrations of Ca, Mn, Sr, sulfate, total dissolved solids and water conductivity values for both the dry season and the wet season. Finally, health risk assessment suggests that Tl may pose non-carcinogenic health risks to local residents over a long time. This study highlights not only anthropogenically-induced but also hidden naturally-occurring Tl enrichment in the hydrosphere of the PRB, and enhances the understanding of aqueous geochemistry of Tl.