Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale constructed wetlands (CWs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the degradation of pollutants through CW systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented CW showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two CWs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of CW sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect.