Submerged macrophytes in constructed wetlands (CWs) can effectively improve wastewater quality. However, the effectiveness of different submerged macrophytes in removing antibiotic-resistant genes (ARGs) from wastewater remains unexplored. Additionally, wastewater loading in wetlands can fluctuate due to climate change, potentially affecting ARG removal efficiency. In this study, we systematically constructed microscale wetlands using three submerged plants: Vallisneria natans (VN), Sagittaria pygmaea (SP), and Myriophyllum spicatum (MS). Their effectiveness in ARGs removal was analyzed at hydraulic retention times (HRTs) of 0, 3, 6, and 9 days under high (HWL) and low (LWL) wastewater loading. The results indicated that under LWL conditions, all ecosystems exhibited a higher reduction rate of ARG diversity and relative abundance (RS) compared to HWL conditions. The efficiency of all ecosystems in reducing ARG diversity and abundance followed the order: MS > VN > SP. The sul resistance gene exhibited the highest RS and was degraded most rapidly in all samples. Additionally, sulfadimidine concentrations significantly decreased under LWL conditions, which was significantly correlated with sul reduction. Chemical oxygen demand, total phosphorus, total nitrogen, ammonium nitrogen, and nitrate nitrogen were identified as key factors influencing bacterial and ARG profiles. The increase in rhizobial bacteria and decrease in aerobic denitrifying bacteria likely contributed significantly to ARGs removal. This study offers new insights into ARG removal by submerged macrophytes in CWs, emphasizing the role of wastewater loading and the potential of MS in enhancing ARG degradation. These findings enhance CW design and management to mitigate ARG contamination in wastewater.