Riparian ecosystems are particularly prone to heavy metal (HM) contamination, acting as a sink for HMs coming from human activities upstream or on adjacent uplands. An advanced understanding of the spatio-temporal dynamics, environmental drivers and the likely sources of HM contamination in riparian soils will be necessary for the conservation of riparian ecosystems. Thus, we conducted a nine-year study across a 600 km stream gradient along the Yangtze river, which has come under immense pressure in recent years partly due to the establishment of the Three Gorges Dam (TGD), the largest hydropower dam in the world. Levels of soil As, Cr, Pb, and Cu in the TGD's water level fluctuation zone (WLFZ) have consistently increased since the TGD's establishment. This increase tended to be more rapid at the upstream reaches of the WLFZ, where most HMs (As, Cd, Pb, Cu, and Zn) also tended to be particularly high. Our analyses suggest that the spatio-temporal dynamics of these metals are strongly influenced by soil phosphorus (P), organic matter, texture and manganese. In many cases HM levels exceeded acceptable pollution levels according to multiple indices. However, from 2008 to 2010 Hg and Cd presented great threat to ecosystem health, but from 2011 to 2016 levels of As and Pb became the primary concern due to increases in their concentrations of 152 and 38%, respectively, relative to 2009 levels. Factor analysis indicated that the major identifiable anthropogenic sources of HMs were traffic exhaust, sources associated with organic matter output (e.g. sewage), and sources associated with P output (e.g. agricultural runoff), with the latter generally dominant in the upper and middle reaches of the TGD watershed. These results indicate that the prioritization of As and Pb pollution and control of agricultural runoff will play an important role in the ecological protection in the TGR's riparian ecosystems.