Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of polluted surface water. However, the diversity and structure of microbial community in surface water constructed wetland system remain poorly known. The present study was made to characterize bacterial and archaeal communities in a surface water constructed wetland using Illumina high-throughput sequencing. The diversity and structure of both bacterial and archaeal communities illustrated a remarkable spatiotemporal variation. Archaeal communities showed lower richness and diversity than bacterial communities. Bacterial diversity decreased with increasing wetland layer depth. A variety of bacterial phyla or candidate divisions were found in wetland bacterial communities, including Proteobacteria, Chloroflexi, Firmicutes, Acidobacteria, Bacteroidetes, Nitrospirae, Actinobacteria, Spirochaetae, Planctomycetes, Chlorobi, Deferribacteres, Cyanobacteria, OP8, WS3, TA06, and OP11, while Proteobacteria, Chloroflexi, and Firmicutes were the major bacterial groups. Euryarchaeota and Thaumarchaeota dominated wetland archaeal communities.