This study reports the geochemical characteristics of zinc (Zn), copper (Cu), lead (Pb), nickel (Ni), mercury (Hg), iron (Fe), and manganese (Mn) in the riparian sediment pore water of the Songhua River, Northeast China. In total, 36 pore water samples and 18 surface water samples from three typical sections were collected and analyzed in June 2009. Cluster analysis of heavy metals was performed to analyze the pollution sources of the metals. Results showed that Hg concentrations in the pore water were greater than those in the surface water, indicating a potential ability of Hg release from riparian sediment system to river water. However, concentrations of Fe and Mn in the surface water were greater than those in the pore water, demonstrating that the microenvironments of riparian and riverbed sediment systems were quite different. Variations of Zn, Cu, Pb and Ni between the surface and the pore water were different in each section. Most metals had similar horizontal and profile distribution characteristics in the three sections except for Zn and Ni. Hg, Fe and Mn concentrations in the pore water increased gradually with the increase in horizontal distance from water body, in contrast to this, Cu decreased, and Pb presented a fluctuating trend. With the increase in depth, Pb and Fe, Cu and Mn showed the same trends, and Hg showed a variable trend. The above distribution characteristics could mainly be attributed to the properties and the interactions of metals, pH and oxidation-reduction conditions, and the complex pollution sources and hydrologic regime in history. The probable sources of metals include the historical and ongoing discharge of industrial wastewater, mining activities, sewage irrigation for agricultural production, and atmospheric deposition from coal-fired plants.