Vegetated drainage ditches (VDD) as a type of constructed wetland primarily serve to remove and store excess water associated with irrigation and storm events. Current research suggests using a VDD as an additional practice in the mitigation of surface water pollution. The VDD for water treatment of the Glinscica River was constructed in 2006. The efficiency of the system was evaluated in 2008 and 2009 regarding the reduction of SS, COD, BOD5, NH4-N, NO3-N, NO2-N, TN, ON and TP. The microbiological association developed in the VDD was analyzed with a focus on the identification and quantification of the narG gene as a denitrification indicator. This paper discusses the efficiency of pollution removal and the distribution of the narG gene within the VDD. The results showed that the highly fluctuating water regime was the main reason for the even distribution and abundance of the narG gene throughout the system, regardless of oxygen saturation or the nutrient status of the wastewater. With the exception of SS, pollutant concentrations met the permitted outflow levels.