Illumina high-throughput sequencing indicated the depth-related change of microbial community richness, diversity,structure in vertical-flow gravel, steel slag or zeolite VF-CW systems. Microbial community was considerably influenced by substrate type. Compared with bacterial community, archaeal community had relatively low richness and diversity. Proteobacteria and Acidobacteria were the largest two bacterial phyla, while Euryarchaeota predominated in archaeal community. Their relative abundance was also affected by substrate type.