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Surface- and ground-water quality in the Chino-Santa Ana River Basin, California is a major source of drinking water supply for the Los Angeles metropolitan area. This water source is significantly degraded due to intensive dairy operations and the disposal of untreated wastewater into the Chino Basin. Constructed wetlands have been recognized as a treatment option for the removal of high concentrations of contaminants in agricultural waste water prior to land application. The goal of this study was to characterize the fate and transport of chemical contaminants and pathogens in a constructed wetland system and to determine the diversity of ammonia oxidizing bacteria that were responsible for nitrogen mineralization in the wetlands. Water samples were collected weekly for 11 months from two wetlands to determine the efficiency of the treatment system in removal of chemical contaminants, total/fecal coliforms and Escherichia coli. Reduction by the treatment was greatest for biological oxygen demand (BOD), suspended solids, chemical oxygen demand (COD), nitrate, and coliforms. There was only moderate removal of total nitrogen and phosphorus. The population of ammonia-oxidizing bacteria showed a higher percentage of Nitrosospira-like sequences from the wetland samples, compared to a higher percentage of Nitrosomonas-like sequences from manure, feces, raw washwater and facultative pond. These results demonstrate that the wetland system is a natural process dependent upon the development and maintenance of healthy microbial communities for optimal wastewater treatment in reducing dairy waste in the Santa Ana watershed quality