To determine whether the discharge control of heavy metals in the Yangtze River basin can significantly change the pollution level in the estuary, this study analyzed the sources (upper river, the estuarine region, and the adjacent sea) of ten heavy metals (As, Cd, Co, Cr, Cu, Hg, Ni, Pb, Sb, and Zn) in dissolved and particulate phases in the surface water of the estuary during wet, normal, and dry seasons. Metal sources inferred from section fluxes agree with those in statistical analysis methods. Heavy metal pollution in the surface water of Yangtze Estuary primarily depends on the sediment suspension and the wastewater discharge from estuary cities. Upper river only constitutes the main source of dissolved heavy metals during the wet season, while the estuarine region and the adjacent sea (especially the former) dominate the dissolved metal pollution in the normal and dry seasons. Particulate metals are mainly derived from sediment suspension in the estuary and the adjacent sea, and the contribution of the upper river can be neglected. Compared with the hydrologic seasons, flood-ebb tides exert a more obvious effect on the water flow directions in the estuary. Sediment suspension, not the upper river, significantly affects the suspended particulate matter concentration in the estuary. Display omitted •City sewage and sediment suspension dominate metal pollution in the Yangtze Estuary.•River runoff significantly affects dissolved metal pollution only in the wet season.•Particulate metals were mainly from sediment suspension in the Yangtze Estuary.•Section fluxes and statistical analysis methods provide identical metal sources.