There is a paucity of knowledge on archaeal community richness and diversity in surface water CW system. Only reported a remarkable spatiotemporal change of archaeal richness and diversity in a pilot-scale surface water VF-CW. However, the change pattern of archaeal richness and diversity in surface water CW remains not understood. In this study, the three VF-CW systems showed similar depth-related change pattern of archaeal diversity. Archaeal diversity was subject to a decrease but then an increase.However, the three VF-CW systems showed different depth-related change pattern of archaeal richness. These results were consistent with those found for bacterial community. Moreover, the present study also provided the evidence for the first time that the substrate effects on CW archaeal richness and diversity were affected by wetland depth. In addition, the richness and diversity of archaeal community were found to be much lower than those of bacterial community. This was in agreement with the result found in a pilot-scale surface water VF-CW. Other previous studies also reported lower archaeal than bacterial diversity in natural wetland and CW system treating municipal wastewater.