The ecological health of the Poyang Lake watershed is an important guarantee for maintaining ecological security in the downstream region of the Yangtze River, while the discharge of industrial wastewater from heavy metal minerals in the Poyang Lake watershed will pose a great threat to the ecological health. The aims of this study were to determine and discuss the pollutant source and transport characteristics of heavy metals in Poyang Lake by monitoring the concentration of eight elements (As, Cr, Fe, Mn, Mo, Pb, Se, and V) in rivers of different scales and evaluate the adverse effects of heavy metals on the ecological health of the Poyang Lake watershed. The results showed that the average Nemero comprehensive pollution index in the Poyang Lake watershed was 2.67, belonging to moderate pollution, and that its pollution indexes were between 4.14 to 4.74 during the high flow period, belonging to severe pollution, which was more serious than during the low flow period. The main polluted elements for the Poyang Lake watershed were V and Se, wherein the maximum concentration of V was 331.90 μg/L, which was 6.64 times higher than the national water quality standard (50 μg/L). The concentrations of heavy metals and the changes in the hydrological characteristics due to seasonal differences were the main factors for controlling the transport flux of heavy metals from the watershed, while the response of transport flux from small scale watershed to the change of flow was more sensitive. The heavy metals transport fluxes from Xiang River to Jiazhu River, Jiazhu River to the Gan River, and the Gan River to the Poyang Lake were 7.30 kg/km², 4.06 kg/km², and 28.10 kg/km², respectively. The output contribution rate of heavy metals downstream in watersheds of different scales was related to runoff. During the high flow period, the contribution rate of Xiang River watershed to the output of heavy metals in Jiazhu River watershed was 1.10%, and that of Jiazhu River watershed to the Gan River watershed was 0.02%. In contrast, during the low flow period, the contribution rate of Xiang River watershed to the output of heavy metals in Jiazhu River watershed and that of Jiazhu River watershed to the Gan River watershed were 1.61% and 0.02%, respectively. Principal component analysis indicated that the main source of dissolved heavy metals in Poyang Lake was industrial mining activities. Thus, the industrial pollution sources should be given priority when preventing and controlling heavy metals pollution of the water body in the Poyang Lake watershed.