Ten metals were analyzed in samples collected in three seasons (the dry season, the early rainy season, and the late rainy season) from two rivers in China. No observed toxic effect concentrations were used to estimate the risks. The possible sources of the metals in each season, and the dominant source(s) at each site, were assessed using principal components analysis. The metal concentrations in the area studied were found, using t-tests, to vary both seasonally and spatially (P = 0.05). The potential risks in different seasons decreased in the order: early rainy season > dry season > late rainy season, and Cd was the dominant contributor to the total risks associated with heavy metal pollution in the two rivers. The high population and industrial site densities in the Taihu basin have had negative influences on the two rivers. The river that is used as a source of drinking water (the Taipu River) had a low average level of risks caused by the metals. Metals accumulated in environmental media were the main possible sources in the dry season, and emissions from mechanical manufacturing enterprises were the main possible sources in the rainy season. The river in the industrial area (the Wusong River) had a moderate level of risk caused by the metals, and the main sources were industrial emissions. The seasonal and spatial distributions of the heavy metals mean that risk prevention and mitigation measures should be targeted taking these variations into account.