<p>Reclaimed water irrigation has been widely adopted to alleviate water scarcity, but the migration characteristics of antibiotic resistance genes (ARGs) in rice soil under different irrigation modes are still unclear. In a greenhouse pot experiment, the effects of irrigation mode [flooding (FI), controlled (CI), and combined (CFI)] and water source (reclaimed vs. clean) on the distribution of antibiotic resistance genes (ARGs) in a soil-rice system were investigated. The results showed that irrigation mode dominates ARG distribution. Bacterial community structure and ARGs composition in soil, roots, and grains varied across water management treatments (FI, CI, and CFI), whereas water source (reclaimed vs. clean) had weaker impact. However, reclaimed water irrigation was associated with higher abundance of ARGs in roots, which decreased under FI, but increased under CI and CFI, mainly due to changes in bacterial structure. pH, NO₃⁻-N, and K⁺ were the major explanatory variable that might cause the bacterial changes. AK is the major explanatory variable causing changes in ARGs. Soil intI1 and six ARGs showed a positive correlation with the dry mass of rice roots, stems, leaves, and ears, but a negative correlation with the dry mass of rice grains. These correlations suggest that the physiological status of the rice plant is associated with the fate of ARGs in the rhizosphere. This study provides empirical insights into the agronomic management of reclaimed water use, highlighting the need to consider irrigation-induced microbial shifts to lower the potential exposure load associated with ARG migration in paddy systems.</p>