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Wastewater (WW) irrigation to agricultural soils is one of the most economical and effective water-saving strategies. The effects of WW irrigation on soil microbial communities have gained increasing focus as these effects are not well understood. In this study, the effects of WW and groundwater (GW) irrigation on microbial diversity and structure were compared using the high-throughput sequencing analysis of 16S rDNA amplicons. Soil samples irrigated by WW for several decades and maize soil (loamy) samples irrigated by GW were collected from Luancheng Town, Shijiazhuang City, China. Compared to the GW groups, WW groups exhibited non-significant soil bacterial community abundance at the 0–20 and 20–40 cm depths. WW irrigation significantly altered the bacterial community composition and structures compared to GW irrigation. The relative abundance of Proteobacteria and Firmicutes increased in WW irrigated soil, while Actinobacteria decreased. Moreover, 14 significantly abundant biomarkers from Proteobacteria and Firmicutes that corresponded with WW irrigation were identified. Additionally, WW irrigation enriched some KEGG pathways that corresponded with metabolism and human diseases. The physical and chemical properties of WW irrigated soil may shape the compositions and structures of soil bacterial communities. The findings of this study illuminated the effects of wastewater irrigation on microbial characteristics, which is important for estimating the effects of long-term wastewater irrigation on soil environmental health. [ABSTRACT FROM AUTHOR]