So far, only one study reported the depth-related change of archaeal community structure in surface water CW system. Information on the influential factors driving archaeal community structure is still lacking. In this study, the result of UPGMA clustering showed a considerable depth-related shift in archaeal community structure in each VF-CW system. Archaeal community structure was found to be influenced by both substrate type and wetland depth. This was consistent with the result observed for bacterial community.