Abstract: Microorganisms play an essential role in material transformation and energy flow in constructed wetland systems. However, the excessive reproduction of microbes would cause the formation of large amounts of extracellular polymers (EPS), which can lead to the clogging in constructed wetlands. This study mainly focused on bacteria and compared its ability to indicate the clogging in constructed wetlands so as to provide some important implications for developing the biological assays to monitor the clogging of constructed wetlands in the future. In order to achieve this, four horizontal subsurface flow constructed wetlands (HFCWs) were designed and operated to simulate the process of clogging and to investigate the interaction between the clogging and microorganism by monitoring the variation of the filtration rate of substrates, the removal efficiency shift of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorous (TP), and bacterial communities by high-throughput sequencing of 16S rDNA. Results showed that as the clogging progression, the filtration rate of substrates and the TP removal efficiency consistently decreased in four wetland systems, while the COD and TN removal efficiency was fluctuated constantly with 50%—85% and 10%—20%, respectively. Sequencing results indicated that the clogging reduced the richness and diversity of bacterial community structure; Proteobacteria, Firmicutes and Chloroflexi were dominated in all HFCWs; the relative abundance of Proteobacteria increased significantly as the clogging developed; more specifically, the abundance of denitrifying bacteria belonging to Proteobacteria (Thauera, Zoogloea and Rhizobium) and organic-metabolizing bacteria belonging to Firmicutes and Chloroflexi (Clostridium sensu stricto, Gracilibacter and Levilinea) increased significantly. These results suggest that the afore-mentioned bacteria were expected to act as early warning indicators for the clogging of constructed wetlands.