Great attention has been paid to the potential of wastewater irrigation as a sustainable water source, particularly due to water scarcity and water pollution issues. However, few studies have focused on its adverse effects and on the health risks it may pose. In this study, the physicochemical properties of soils and plants irrigated with rural domestic wastewater and associated microbiological risks were investigated. The results showed that sewage irrigation could increase the production of vegetables and improve soil fertility. While the nitrate content of plants increased significantly, pathogens on plants and in soils increased after irrigation with raw wastewater. In particular, there was a wide range of pathogenic bacteria in the phyllosphere, which may indicate risks if contaminated vegetables are consumed directly. Treated wastewater irrigation was not significantly different from controls, which were irrigated by tap water; consequently, it can be used as an alternative water resource for agricultural irrigation. The presence of a wide spectrum pathogens in wastewater shows the necessity of long-term monitoring and further evaluation.