During rainfall, phosphorus in drainage pipe sediments is easily washed and released. This study investigates the migration of phosphorus between sediments and water in storm and sewage sewers, the microbial community structure in sediments, and phosphorus transformation under biological action. Results showed that when the initial concentration of phosphorus in stormwater (water column) in storm sewer was high (1-2mg/L), the total phosphorus (TP) level decreased in the water column but increased in the sediments, showing a trend of phosphorus migration from the water column to the sediments. Moreover, under high concentration (2mg/L), the TP level decreased by 83.19% in the water column within 210min, which was greater than 64.9% of the medium-concentration stormwater (1mg/L). In sewage sewer, when the initial concentration of phosphorus in sewage was about 2mg/L, phosphorus would migrate from the sediments and interstitial water to the water column because of the high concentration of phosphorus in the sediments. In addition, the variation in phosphorus was caused not only by concentration gradient but also by microbial communities. Phosphate accumulating organisms, such as Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, existed in the storm and sewage sewers, which could ingest dissolved reactive phosphorus in the water column and interstitial water and convert it into phosphorus in organisms. In storm sewers, Acidimicrobiia transferred phosphorus from the water column and interstitial water to the sediments through biochemical reactions and physical adsorption. In sewage sewers, organic acids secreted by Clostridia, Bacteroidia, and Bacilli could dissolve some insoluble phosphorus in sediments and then transfer them to interstitial water.