A pilot-scale horizontal subsurface flow constructed wetland (HSSFCW) was operated to purify industrial runoff containing polycyclic aromatic hydrocarbons (PAHs) in Guangzhou, China. Synthetic industrial runoff was fed into the HSSFCW with continuous flow at an average loading rate of 0.128 m(3)/(m(2)/day) for about 2 years. Pollutants such as chemical oxygen demand (COD), total phosphorus (TP), and phenanthrene were mainly removed in the front quarter of the HSSFCW, and in the vertical direction, the average removal rates of COD, TP, total nitrogen (TN), ammonia, and phenanthrene of the upper layer were 64.23, 71.16, 50.81, 65.38, and 92.47 %, which were 1.23, 2.08, 1.48, 1.72, and 1.17 times higher than those of the bottom, respectively. Correlations among pollutant removal, soil environmental indexes, enzyme activities, and soil microbial community structure were evaluated. Enzyme assays (dehydrogenase, catalase, nitrate reductase, and polyphenol oxidase) showed significant associations between enzyme activities and pollutant removal (p < 0.01 and p < 0.05). Soil microbial community structure was assessed with denaturing gradient gel electrophoresis (DGGE) fingerprinting method, and results demonstrated that bacterial communities remained relatively stable in different seasons. Proteobacteria and Bacteroidetes were found to be the dominant phyla of the bacteria communities, and three clones which might be related to the biodegradation of phenanthrene were also detected. Results of the present work would broaden the knowledge of the purification mechanism of contaminants in the constructed wetlands (CWs), and identification of the treatment performances and temporal and spatial variations of biological activities of subsurface flow constructed wetlands (SSFCWs) would help to improve the operations of CWs for surface water protection.