Organic micropollutants (OMPs) facilitate the spread of antibiotic resistance genes (ARGs). Ammonia-oxidizing microorganisms (AOMs) are crucial for OMP degradation during riverbank filtration (RBF) and significantly influenced by NH4+-N concentrations. However, the effect of NH4+-N on OMP removal and ARG occurrence in RBF remains unclear. This study aimed to examine the effects of low (∼0.1 mg/L) and high (∼2.2 mg/L) NH4+-N concentrations on OMP removal, ARG occurrence, and microbial communities. NH4+-N addition had no significant effect on the removal of 108 out of 128 OMPs, suggesting that other factors primarily govern the removal process. Notably, NH4+-N addition enhanced the removal of 20 OMPs by 3–70%, including three quinolones (e.g., flumequine), indicating its promotion of specific OMP removals. This effect may primarily result from NH4+-N enhancing OMP biotransformation through the stimulation of AOMs (particularly AOA and comammox) and heterotrophs (e.g., Bradyrhizobium). Furthermore, NH4+-N addition significantly reduced the abundance of eight ARGs, including quinolone ARGs, likely due to its inhibition of antibiotic-resistant bacteria. Additionally, we hypothesize that NH4+-N alleviates OMP selective pressure on microorganisms by promoting OMP conversion through AOMs. This study enhances the understanding of microbe-mediated OMP removal in the presence of NH4+-N and its impact on ARG occurrence during RBF.