Proteobacteria might play important roles in biodegradation of organic compounds in CW system. Several previous studies have showed the dominance of proteobacterial organisms in surface water CW system. In this study, Proteobacteria was found to be the largest bacterial phylum group in each VF-CW system, but its proportion showed different depth-related change pattern. also indicated that either sand or zeolite CW systems showed more evident depth-related shift in proteobacterial proportion than gravel CW system. Substrate type might have a strong effect on proteobacterial community structure in surface water CW system. The result obtained in this study further confirmed the influence of substrate type on CW proteobacterial community structure. Several previous studies showed the relative abundance of Acidobacteria in surface water CW system, yet its influential factors remain elusive. In this study, different depth-related change patterns of Acidobacteria proportion were found in three surface water VF-CW systems. In addition, the present study provided the evidence for the first time that Acidobacteria proportion in surface water CW system could be influenced by substrate type.