Heavy metal toxicity in aquatic sediments increases over time because inorganic contaminants are not biodegradable. Phytoremediation of industrial waste is becoming common practice. However, there is limited research to characterize phytoremediation by native plants to better understand pollutant remediation in existing wetlands and for wetland restoration. In southern California, stormwater runoff now constitutes the largest contributor of heavy metals to waterways and the ocean. Recent research has shown that microbial activity in the root zone of wetland plants can enhance phytoremediation of heavy metals. The goal of this study was to identify native wetlands plants that demonstrate a strong relationship with the soil microbial community and then evaluate their potential to immobilize heavy metal pollution in natural settings. During a year-long field study, hydrologic conditions, sediment, soil pore water and plant tissue associated with five native wetland plants along a two-mile stretch of the Santa Margarita River in southern California were analyzed for oxidation-reduction potential, dissolved organic carbon, microbial biomass and activity, and heavy metals (Cr, Cu, Pb, and Zn) content. Salix lasiolepis had significantly higher concentrations of all heavy metals in its associated sediment compared to other species. Soil organic matter was strongly correlated with metal content in the sediment and S. lasiolepis had twice as much soil organic matter as the other species. Schoenoplectus californicus had significantly more Cr in leaf tissue than other species. Subsequently, S. lasiolepis and S. californicus were tested in a greenhouse experiment for immobilization and uptake of Cr. Though soil organic matter was the same among all pots in the greenhouse experiment, the same results were found. S. lasiolepis immobilized more Cr in the soil and S. californicus had more Cr in leaf tissue. Immobilization of Cr in soil from S. lasiolepis pots was associated with more reducing soil conditions and an anaerobic, metal-reducing soil microbial community. S. californicus plants was associated with more oxidized soil conditions, a more aerobic soil microbial community and greater uptake of Cr into leaf tissue. These findings suggest that S. lasiolepis is a good candidate for further study of heavy metal phytoremediation in riparian wetlands.