Abstract The technology for the activation of irrigation brackish water was successful at improving the soil environment and crop yields. However, very few studies have examined how activated brackish water irrigation affects the rhizosphere bacterial communities and network patterns. By combining 16S rRNA high-throughput sequencing, we evaluated the diversity and composition of the rhizosphere bacterial community after being subjected to different types of irrigation with activated brackish water. We also analyzed the correlation and co-occurrence networks among the bacterial diversity, composition, and rhizosphere soil properties. The results showed that compared with brackish water irrigation, the salt content of activated irrigation water significantly decreased by 9.35%, 9.83%, and 12.95%, respectively. Irrigation with different types of activated brackish water had no significant (p > 0.05) effect on the diversity of the rhizosphere bacterial community, but it significantly changed its community composition, which was primarily dominated by soil nutrient indicators. The soil total nitrogen (TN) showed a significant (p < 0.01) negative correlation with the Chao1 index. Additionally, the changes in bacterial communities under different types of activated brackish irrigation water mainly occurred at the genus level. We showed that the rhizosphere soil that had been irrigated with oxygenated brackish water and magnetized brackish water better supported the reproduction of some soil-borne pathogens. Magnetization-oxygenation coupling treatment could significantly reduce the colonization of soil-borne pathogens of the rhizosphere soil, while also favoring the function of functional bacteria involved in soil nutrient transformation. This study highlights the main factors affecting the rhizosphere soil bacterial community structure by activated brackish water irrigation, while also providing new technical support for brackish water irrigation.