In view of the unclear microbial mechanism of polluted sediment remediation in urban rivers under low water level operation, a study on the characteristics and influencing factors of microbial communities in the polluted sediment of urban rivers under low water level operation was conducted based on the physical and chemical property analysis, metagenomic high-throughput sequencing, and bioinformatics analysis of sediment in different urban rivers at high and low water levels. It is found that Proteobacteria, Actinobacteria, Firmicutes, and Euryarchaeota are the bacteria and archaea with the highest relative abundance under different water level operating conditions, respectively. The Shannon index of bacteria in the sediment under high water level operation is significantly higher than that under low water level operation