The Prado Wetlands in Chino, CA is a free water surface (FWS) constructed wetland consisting of 50 shallow ponds that treats approximately 70% of Santa Ana River water prior to its passage to Orange County, CA where it is used for groundwater recharge. The Santa Ana River is an effluent dominated body of water that receives natural mountain runoff and tertiary wastewater from various municipalities within the Santa Ana River watershed. The main function of Prado Wetlands has been the removal of nitrate-nitrogen. The method of removal is a combination of microbial and plant processes. A year long study was conducted to understand the changes in water chemistry and microbial composition of the wetlands as affected by different concentrations of plants per wetland pond. Community profile using DGGE of total DNA was used to determine microbial composition in different sections of the wetland and total RNA (cDNA) was used to identify members of the metabolically active microbial populations associated with the wetland microbial communities. There was a substantial fluctuation in nitrate and orthophosphate levels throughout the summer and fall. The ponds with 50% plant cover had as high as 99% nitrate removal. The average change between the influent and effluent was 50-60% nitrate removal and 40-50% orthophosphate removal. There was little change in the heterotrophic bacterial counts, but a substantial drop of about two to three log for both E. coli and Enterococcus. DGGE analysis showed that there were 11 species that were found in both the influent and effluent bacterial populations.