Dissolved heavy metals are not only the essential micronutrients, but also the toxic elements for human bodies. To investigate the heavy metal sources and assess the water quality of the Lancangjiang River, dissolved Cr, Ni, Cu, Zn, Mo, and Pb were detected in this study. The results show that dissolved Ni and Mo, Cr and Pb, and Cu and Zn were similarly distributed within the drainage basin. The correlation analysis exhibited that dissolved Ni and Mo had correlation with water parameter, and dissolved Cu was weakly correlated with Ni, indicating that they might be affected by natural processes. The principal component analysis explained 68.342% of the total variance for three principal components, of which dissolved Ni, Mo, and Cu were controlled by natural inputs; dissolved Cu and Cr were affected by anthropogenic activities; and dissolved Zn was influenced by agricultural activities in the downstream. The water quality showed that the water in upstream was worse than in midstream and downstream, and the whole drainage basin had water of excellent quality. Water within the drainage basin poses no risks to human bodies via daily diets and dermal routes. Dissolved Zn, Cu, and Mo occupied the major proportion of heavy metals transporting into the Mekong River. The agricultural inputs of dissolved Zn might pose potential risks to the Mekong River.