Recently, there has been increasing interest in the use of rain garden systems as environmentally friendly ecological infrastructures for controlling stormwater runoff and managing non-point source pollution and information for the contamination of soil and plants can be essential for sustainable rain garden management. In this study, four rain garden mesocosms, namely single species planting with Rhododendron lateritium, single species planting with Zoysia japonica, mixed planting with R. lateritium and Z. japonica, and control without plants, were tested to investigate the change in concentrations of nutrients (N and P) and heavy metals (Cd, Cu, Pb, and Ni) in the soil and plants used in the rain garden system. The presence of plants resulted in greater nutrient retention in soil and lower potential leaching from the system. All systems showed an increase in the heavy metal concentrations in soil. The concentrations of most heavy metals were found to be higher in the herbaceous plants (Z. japonica) than in the shrubs (R. lateritium). The belowground part (root) had higher heavy metal concentrations than the aboveground part (leaf) but also showed a potential increase in leaves, and hence, careful plant management should be considered during rain garden operation.