Thallium (Tl) is an extremely toxic metal with high risk. Sediment samples from a well dated sediment core retrieved from a heavily polluted urban lake were measured to assess the magnitude of Tl pollution and reveal its transfer mechanisms within the lake. The results show that the lake has experienced serious Tl pollution during the past 60 years, owing to a large influx of Tl-bearing wastes mostly from a neighboring copper (Cu) smelter. The Tl contents in the sediment core at different depths generally correlated positively with the production scale of Cu smelting activities in the past. Further mineralogical analysis on the electrostatic precipitator dust from the Cu smelter and highly-polluted samples from the sediment core by electronic microscopy and X-ray diffraction suggested that Tl was primarily bound to quartz and aluminosilicates. Large quantities of Tl were also observed in diatom frustules collected from the sediments, suggesting a potentially significant role of biogenic silicates in the uptake and transfer of Tl in the sediment-water system. The findings indicate a new and emerging pollution source of thallium arising from copper metallurgy activities. The results also highlight the necessity of strengthened monitoring and regulations towards Tl pollution in environmental systems impacted by Cu smelting activities in China and other nations.