Based on the monitoring data of 18 river sections, this study investigated the spatiotemporal distribution, sources and ecological risks of 8 heavy metal ions in the upper reaches of Wujiang River, and analyzed the influence of dissolved organic matter (DOM) on the migration and distribution of heavy metals. The results showed that the overall content of heavy metals in the upper reaches of Wujiang River was low with significant seasonal variations, and the average concentrations of Cr, Fe, Co, Ni, Cu, As, Cd and Sb were 0.71, 19.20, 0.17, 1.09, 0.73, 0.65, 0.06 and 1.22 μg/L, respectively, which were all lower than the level of Class III of the Environmental Quality Standard for Surface Water. Principal component analysis revealed a homology among Cr, Fe, Co, Ni, Cd and Sb, primarily sourced from natural origins. Cu was additionally affected by industrial activities including electroplating, printing and dyeing, while as was partially originated from the application of pesticides and fertilizers. Heavy metals showed positive correlations with DOM and its fluorescent components C1–C4, indicating that DOM could promote the migration and enrichment of heavy metals in water. Cr, Fe, Co, Ni and Sb showed significant positive correlation with DOM characteristic parameters SUVA254 and BIX, further confirming that DOM with higher aromaticity and biological reactivity showed higher metal affinities. The evaluation results of single factor and Nemerow comprehensive pollution index suggested that the pollution level of heavy metals in the upper reaches of the Wujiang River retained relatively low, rendering it an ideal source of drinking water. However, the potential ecological risks of heavy metals under the influence of DOM need more concern.