In Taipu River, after being transformed from a drainage channel to a drinking water supply river in 1995, heavy metals that have accumulated in sediments have become an environmental issue. Herein, we collected sediments of Taipu River in 2018, 2020, and 2021 and analyzed the distribution of Sb, As, Cd, Cu, Pb, Cr, and Zn to identify their sources. The results revealed that the mean concentrations of heavy metals were above the background values, except for Cr and As. During the non-flood season, the midstream of Taipu River becomes a heavy metal hotspot, with their concentrations 2–5 times higher than those in upstream sediment. There were significant correlations (r = 0.79–0.99) among drainage, precipitation and flow rate, which indicated that drainage caused by both the opening of Taipu Gate and precipitation control the flow rate and, then, possibly influenced the distribution of heavy metals. Moreover, three sources (industrial sources, particle deposition sources, and natural sources) were characterized as the determinants for the accumulation of heavy metal by the Positive Matrix Factorization model, with the contribution rates of 41.7%, 32.9%, and 25.4%, respectively. It is recommended that the influence of hydrological conditions and industrial activities should be a key consideration when developing regulations for the management of heavy metals in rivers.