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In Taiwan, more than 20% of the major rivers are mildly to heavily polluted by domestic, industrial, and agricultural wastewaters due to the low percentage of sewers connected to wastewater treatment plants. Thus, constructed or engineered wetlands have been adopted as the major alternatives to clean up polluted rivers. Constructed wetlands are also applied as the tertiary wastewater treatment systems for the wastewater polishment to meet water reuse standards with lower operational costs. The studied Kaoping River Rail Bridge Constructed Wetland (KRRBCW) is the largest constructed wetland in Taiwan. It is a multi-function wetland and is used for polluted creek water purification and secondary wastewater polishment before it is discharged into the Kaoping River. Although constructed wetlands are feasible for contaminated water treatment, wetland sediments are usually the sinks for organics and metals. In this study, water and sediment samples were collected from the major wetland basins in KRRBCW. The investigation results show that more than 97% of total coliforms (TC), 55% of biochemical oxygen demand (BOD), and 30% of nutrients [e.g. total nitrogen (TN), total phosphorus (TP)] were removed via the constructed wetland system. However, results from the sediment analyses show that wetland sediments contained high concentrations of metals (e.g. Cu, Fe, Zn, Cr, and Mn), organic contents (sediment oxygen demand = 1.7 to 7.6 g O(2)/m(2) d), and nutrients (up to 18.7 g/kg of TN and 1.22 g/kg of TN). Thus, sediments should be excavated periodically to prevent the release the pollutants into the wetland system and causing the deterioration of wetland water quality. Results of polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and nucleotide sequence analysis reveal that a variation in microbial diversity in the wetland systems was observed. Results from the DGGE analysis indicate that all sediment samples contained significant amounts of microbial ribospecies, which might contribute to the carbon degradation and nitrogen removal. Gradual disappearance of E. coli was also observed along the flow courses through natural attenuation mechanisms.