Rivers integrate natural and anthropogenic mercury (Hg), and are important vectors of terrestrial Hg to the oceans. Here, we report the total Hg concentration and Hg isotope compositions of dissolved load in the Pearl River, the second largest river in China, in order to understand the processes and sources affecting Hg systematics in large anthropogenically-impacted river water. The dissolved Hg showed a concentration varying from 0.45 to 2.44 ng/L, within the range reported for natural background lake and river waters. All river water samples showed significantly negative δHg (-2.89‰ to -0.57‰), slightly positive ΔHg (-0.05‰ to 0.52‰), and mostly positive ΔHg (0.10‰ to 0.57‰), except for three extremely negative values (-2.25‰ to -0.76‰). Combined with other geochemical parameters, we suggest that the influence of in-river processes, such as sorption and reduction, on the Hg isotope compositions is very limited, and the dissolved Hg in the Pearl River mainly comes from atmospheric precipitation and surface soil weathering. Although the whole river basin is largely affected by urban, industrial and mining activities, unlike other heavy metals, their direct contributions to dissolved Hg seem limited. It is worth noting that the three samples with very negative ΔHg values (down to -2.25‰) are derived from special source which attribute to the input of Hg released from the local incineration of electronic wastes. This study demonstrates that isotope approach is a powerful tool for tracing sources and pathways of Hg in large complex river systems.