The treatments of swine wastewater with variable hydraulic loading rates (HLRs) and infiltrator structure were investigated using a modified two‐stage constructed rapid infiltration system (CRIS). Furthermore, microbial community distribution at different HLRs in the CRIS was also analyzed by high‐throughput sequencing. Results indicated that when the HLR was 5.44 cm/day and 10.88 cm/day, the removal rate of chemical oxygen demand (COD) was between 68% and 73%. However, the removal rate of COD dropped to 22.3% when the HLR increased to 16.33 cm/day. Compared to the small CRIS, the removal rate of NH3‐N was stable at about 78% in the large CRIS that had ventilation in the middle of the column. In addition, at HLR 11 cm/day, majority of the taxa detected in the CRIS were assigned to Proteobacteria, Firmicutes, and Bacteroidetes. Anaerobic ammonium oxidation occurred in the middle and lower parts of the columns of CRIS. When the HLR increased to 22 cm/day, the abundance of Planctomycetes decreased from 57.48% to 38.88% in the upper layer of the first column, whereas the abundance of Firmicutes increased from 6.8% to 16.17%. Results showed the microbial community shift was observed at different HLR, influencing the pollutants removal rate. © 2019 American Institute of Chemical Engineers Environ Prog, 38: e13218, 2019