We studied enrichment of heavy metals (V, Zn, Cr, Ni, Cu, Pb, As, Sb, and Cd) in a rural stream of the Kuji River basin in central Japan in suspended particulate matter, and associated transport flux during two rainfall events (in November 2003 and in April 2008). The concentration of heavy metals in suspended particulate matter (SPM) exhibited a distinctive temporal variation, wherein the concentrations decreased with increasing water discharge and then increased as the discharge decreased. Concentration of dissolved metal forms showed a slight increase with scatters around the flow rate peak. Enrichment factors for those metals in the SPM decreased sharply as the flow rate increased, making an obvious concave shaped curve (the November 2003 rainfall event). The metal enrichment factors under low flow conditions had a similarity to those found in atmospheric deposits at a foot of the Kuji River basin, suggesting atmospheric source would contribute to enriching the SPM with those metals in part. Mineralogical analyses and carbon content analysis (the April 2008 rainfall event) of the SPM suggests the SPM matrix became more lithological as the flow rate increased. The changes observed in the matrix are thought to be directly related to progressive changes in metal enrichment within the SPM. Concerning the transport phase of several heavy metals, a dynamic change in transport phase partitioning within a rainfall event was suggested. The present enrichment factor study and the SPM matrix characterization implied the partitioning change is due to an increase in lithologic solids during high flow conditions.