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Constructed Wetlands (CW) play a crucial role in the treatment of urban stream water, domestic and industrial wastewater. Their biocenosis of microorganisms is capable of degrading various pollutants, including organic compounds, toxicants and xenobiotics. The object of study was Free Water Surface Constructed Wetland in Moscow, it receives some stormwater and some industrial effluents. We have done study of the transformation of ubiquitous organic contaminants, coming with stormwater to wetland systems: polycyclic aromatic hydrocarbons, phthalates, surfactants, petroleum hydrocarbons. There were used methods of chemical analysis: GC-MS (Agilent GC 6890 MSD 5970, Agilent Technologies USA), HPLC (Agilent 1200, Agilent Technologies USA). Using 16S rRNA gene sequencing approach, we performed the analysis of the bacterial community structure of the sludge and wastewater. DNA isolation was performed using PowerSoil® DNA Isolation Kit (MO BIO Laboratories, CA USA) according to the manufacturer‘s protocol. We used 16 rRNA PCR amplification primers fused with GS Junior sequencing adapters. Taxonomic annotation of the sequences was performed using Ribosomal Database Project (RDP) Classifier tool. We also present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data (http://metacyc.org/). We developed XeDetect software which implements this approach (https://sourceforge.net/projects/xedetect). XeDetext represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool can help to optimize bioreactor performance and avoid some most common technical problems.