The nitrogen removal effect of traditional bioretention cells on runoff rainwater is not stable. The nitrogen removal effect of bioretention cells can be improved by setting up a layered filling structure, but the effect of changes in filling structure on the nitrogen removal process and microbial community characteristics is still unclear. Two types of porosity fillers were set up in the experiment, and a homogeneous bioretention cell and three bioretention cells with layered fillers were constructed by changing the depth range of the upper and lower layers to analyze the influence of the pore variation of different depth fillers on the nitrogen removal process and microbial community characteristics. The experimental results showed that, compared with the homogeneous filing structure, the layered filling structure can strengthen the adsorption of NH4+-N and the conversion of NO3−-N, so as to increase the removal rates of NH4+-N and NO3−-N by 20.71–81.56% and 9.25%–78.19%, respectively. Although the low porosity filler structure will reduce the nitrification activity and urease activity by 48.63%–66.68% and 8.00%–20.64% respectively, it can increase the denitrification activity by 19.14%–31.92%, thus significantly reducing the nitrate content in the filler. The low porosity filler structure can affect the growth and reproduction of various phylum bacteria such as Proteobacteria, Chloroflexi, Acidobacteria, and genus bacteria such as Nitrospira, Ellin6067, Rhizobacter, Pseudomonas, which can improve the diversity and richness of microorganisms.
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